Triad DDG Calculations with Phoenix for 2GI9
Abstract
Use the triad software to calculated the DDG of unfolding for 2GI9 with the phoenix score function
Submission Details
ID: cymFhTUN3
Submitter: Connie Wang
Submission Date: April 7, 2017, 6:02 p.m.
Version: 1
Publication Details
Wang Connie (2017-04-05) Triad DDG Calculations with Phoenix for 2GI9; unpublished work from Protabit groupAdditional Information
Study Summary
| Number of data points | 556220 |
| Proteins | Immunoglobulin G-binding protein G |
| Unique complexes | 556220 |
| Assays/Quantities/Protocols | Computational Protocol: Single Mutant DDG ; Computational Protocol: Double Mutant DDG |
| Libraries | Single Mutants ; Double mutants |
Structure view and single mutant data analysis
Study data
| Colors: | D | E | R | H | K | S | T | N | Q | A | V | I | L | M | F | Y | W | C | G | P |
|---|
Data Distribution
Studies with similar sequences (approximate matches)
Correlation with other assays (exact sequence matches)
Relevant PDB Entries
| Structure ID | Release Date | Resolution | Structure Title |
|---|---|---|---|
| 2MBB | 2014-06-04 | Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex | |
| 2KHW | 2010-02-23 | Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex | |
| 1Q10 | 2003-10-14 | Ensemble of 40 Structures of the Dimeric Mutant of the B1 Domain of Streptococcal Protein G | |
| 1ZXH | 2005-11-08 | G311 mutant protein | |
| 2LUM | 2012-08-29 | Three-State Ensemble obtained from eNOEs of the Third Immunoglobulin Binding Domain of Protein G (GB3) | |
| 5UCE | 2017-08-23 | Solution NMR structure of the major species of DANCER-2, a dynamic and natively folded pentamutant of the B1 domain of streptococcal protein G (GB1) | |
| 6HKA | 2019-03-27 | The solution structure of the micelle-associated FATC domain of the human protein kinase ataxia telangiectasia mutated (ATM) | |
| 1GB4 | 1998-07-22 | HYPERTHERMOPHILIC VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PROTEIN G, NMR, 47 STRUCTURES | |
| 1GJT | 2001-08-09 | Solution structure of the Albumin binding domain of Streptococcal Protein G | |
| 1P7E | 2003-08-05 | GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings | |
| 2N9L | 2016-12-28 | 1H, 13C, and 15N Chemical Shift Assignments for in-cell GB1 | |
| 2NMQ | 2006-11-21 | Simultaneous determination of protein structure and dynamics using rdcs | |
| 2KQ4 | 2009-11-17 | Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy | |
| 5UBS | 2017-08-23 | Solution NMR Structure of NERD-S, a natively folded pentamutant of the B1 domain of streptococcal protein G (GB1) with a solvent-exposed Trp43 | |
| 1GB1 | 1993-04-15 | A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G | |
| 2N7J | 2015-10-14 | Sidechain chi1 distribution in B3 domain of protein G from extensive sets of residual dipolar couplings | |
| 2RPV | 2009-09-15 | Solution Structure of GB1 with LBT probe | |
| 1GJS | 2001-08-09 | Solution structure of the Albumin binding domain of Streptococcal Protein G | |
| 2RMM | 2007-12-04 | Solution structure of GB1 A34F mutant | |
| 2KN4 | 2010-08-18 | The structure of the RRM domain of SC35 | |
| 2K0P | 2009-03-03 | Determination of a Protein Structure in the Solid State from NMR Chemical Shifts | |
| 2KLK | 2009-10-06 | Solution structure of GB1 A34F mutant with RDC and SAXS | |
| 1MPE | 2002-10-30 | Ensemble of 20 structures of the tetrameric mutant of the B1 domain of streptococcal protein G | |
| 1LE3 | 2002-04-24 | NMR Structure of Tryptophan Zipper 4: A Stable Beta-Hairpin Peptide Based on the C-terminal Hairpin of the B1 Domain of Protein G | |
| 2I2Y | 2006-12-12 | Solution structure of the RRM of SRp20 bound to the RNA CAUC | |
| 5UCF | 2017-08-23 | Solution NMR-derived model of the minor species of DANCER-2, a dynamic and natively folded pentamutant of the B1 domain of streptococcal protein G (GB1) | |
| 2IGG | 1994-01-31 | DETERMINATION OF THE SOLUTION STRUCTURES OF DOMAINS II AND III OF PROTEIN G FROM STREPTOCOCCUS BY 1H NMR | |
| 3GB1 | 1999-06-23 | STRUCTURES OF B1 DOMAIN OF STREPTOCOCCAL PROTEIN G | |
| 5UB0 | 2017-08-23 | Solution NMR Structure of NERD-C, a natively folded tetramutant of the B1 domain of streptococcal protein G (GB1) | |
| 2KBT | 2009-02-03 | Attachment of an NMR-invisible solubility enhancement tag (INSET) using a sortase-mediated protein ligation method | |
| 2KWD | 2010-06-02 | Supramolecular Protein Structure Determination by Site-Specific Long-Range Intermolecular Solid State NMR Spectroscopy | |
| 2KHU | 2010-02-23 | Solution Structure of the Ubiquitin-Binding Motif of Human Polymerase Iota | |
| 1FCL | 2001-09-19 | DELTA1.5: A COMPUTATIONALLY DESIGNED CORE VARIANT OF THE B1 DOMAIN OF STREPTOCOCCAL PROTEIN G | |
| 2N9K | 2016-12-28 | 1H, 13C, and 15N Chemical Shift Assignments for in vitro GB1 | |
| 2LGI | 2011-10-26 | Atomic Resolution Protein Structures using NMR Chemical Shift Tensors | |
| 1FD6 | 2001-09-19 | DELTA0: A COMPUTATIONALLY DESIGNED CORE VARIANT OF THE B1 DOMAIN OF STREPTOCOCCAL PROTEIN G | |
| 2J53 | 2007-09-25 | Solution Structure of GB1 domain Protein G and low and high pressure. | |
| 2PLP | 2007-05-08 | Ultra high resolution backbone conformation of protein GB1 from residual dipolar couplings alone | |
| 2GB1 | 1993-04-15 | A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G | |
| 2JU6 | 2007-12-04 | Solid-State Protein Structure Determination with Proton-Detected Triple Resonance 3D Magic-Angle Spinning NMR Spectroscopy | |
| 2J52 | 2007-09-25 | Solution Structure of GB1 domain Protein G and low and high pressure. | |
| 6NJF | 2019-08-21 | Solution NMR Structure of DANCER3-F34A, a rigid and natively folded single mutant of the dynamic protein DANCER-3 | |
| 1PN5 | 2003-10-07 | NMR structure of the NALP1 Pyrin domain (PYD) | |
| 2IGH | 1994-01-31 | DETERMINATION OF THE SOLUTION STRUCTURES OF DOMAINS II AND III OF PROTEIN G FROM STREPTOCOCCUS BY 1H NMR | |
| 6HPJ | 2020-11-18 | Structure of human SRSF1 RRM1 bound to AACAAA RNA | |
| 2JSV | 2008-04-15 | Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy | |
| 1P7F | 2003-08-05 | GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings | |
| 3FIL | 2009-08-18 | 0.88 | Structural and energetic determinants for hyperstable variants of GB1 obtained from in-vitro evolution |
| 2QMT | 2007-12-25 | 1.05 | Crystal Polymorphism of Protein GB1 Examined by Solid-state NMR and X-ray Diffraction |
| 6CHE | 2019-07-10 | 1.1 | Selenomethionine mutant (A34Sem) of protein GB1 examined by X-ray diffraction |
| 1IGD | 1994-11-01 | 1.1 | THE THIRD IGG-BINDING DOMAIN FROM STREPTOCOCCAL PROTEIN G: AN ANALYSIS BY X-RAY CRYSTALLOGRAPHY OF THE STRUCTURE ALONE AND IN A COMPLEX WITH FAB |
| 2IGD | 1998-07-29 | 1.1 | ANISOTROPIC STRUCTURE OF PROTEIN G IGG-BINDING DOMAIN III AT 1.1 ANGSTROM RESOLUTION |
| 6CPZ | 2019-07-10 | 1.12 | Selenomethionine mutant (I6Sem) of protein GB1 examined by X-ray diffraction |
| 2GI9 | 2006-04-25 | 1.14 | Backbone Conformational Constraints in a Microcrystalline U-15N-Labeled Protein by 3D Dipolar-Shift Solid-State NMR Spectroscopy |
| 3MP9 | 2011-02-23 | 1.2 | Structure of Streptococcal protein G B1 domain at pH 3.0 |
| 6CNE | 2019-07-10 | 1.2 | Selenomethionine variant (V29SeM) of protein GB1 |
| 6CTE | 2019-07-10 | 1.2 | 77Se-NMR probes the protein environment of selenomethionine |
| 6C9O | 2019-07-10 | 1.2 | Selenomethionine mutant (V29Sem) of protein GB1 examined by X-ray diffraction |
| 6OC7 | 2020-02-05 | 1.3 | HMP42 Fab in complex with Protein G |
| 6NLA | 2019-01-23 | 1.34 | Crystal structure of de novo designed metal-controlled dimer of B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-zinc |
| 2ON8 | 2007-12-04 | 1.35 | Gbeta1 stabilization by in vitro evolution and computational design |
| 6NL7 | 2019-01-23 | 1.4 | Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q) |
| 6NL6 | 2019-01-23 | 1.4 | Crystal structure of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) |
| 6NL8 | 2019-01-23 | 1.5 | Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-zinc |
| 5BMH | 2016-04-06 | 1.6 | Nitroxide Spin Labels in Protein GB1: T44 Mutant, Crystal Form B |
| 1PGX | 1992-07-15 | 1.66 | THE 1.66 ANGSTROMS X-RAY STRUCTURE OF THE B2 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON TO THE NMR STRUCTURE OF THE B1 DOMAIN |
| 6NL9 | 2019-01-23 | 1.7 | Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-apo |
| 2ONQ | 2008-01-08 | 1.7 | Gbeta1 stabilization by in vitro evolution and computational design |
| 6L9D | 2020-08-12 | 1.73 | X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11S |
| 4OZB | 2014-07-16 | 1.8 | Backbone Modifications in the Protein GB1 Helix: beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35 |
| 5HG2 | 2016-02-24 | 1.8 | Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-2-Asn35 |
| 6L91 | 2020-08-12 | 1.84 | X-ray structure of synthetic GB1 domain with the mutation K10(DVA) |
| 6KMC | 2019-10-23 | 1.84 | Crystal structure of a Streptococcal protein G B1 mutant |
| 6LJI | 2020-08-12 | 1.84 | X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11V |
| 6W00 | 2020-07-29 | 1.85 | Crystal structure of Fab239 in complex with NPNA2 peptide from circumsporozoite protein |
| 1PGB | 1994-04-30 | 1.92 | TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCCOCAL PROTEIN G AND COMPARISON WITH NMR |
| 5HFY | 2016-02-24 | 1.95 | Backbone Modifications in the Protein GB1 Helix: beta-2-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35 |
| 4KGS | 2013-09-04 | 1.95 | Backbone Modifications in the Protein GB1 Loops: beta-3-Val21, beta-3-Asp40 |
| 1QKZ | 2000-02-06 | 1.95 | Fab fragment (MN14C11.6) in complex with a peptide antigen derived from Neisseria meningitidis P1.7 serosubtype antigen and domain II from Streptococcal protein G |
| 6L9B | 2020-08-12 | 1.95 | X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11A |
| 4KGR | 2013-09-04 | 2.0 | Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35 |
| 4KGT | 2013-09-04 | 2.0 | Backbone Modifications in the Protein GB1 Turns: Aib10, D-Pro47 |
| 1EM7 | 2002-05-08 | 2.0 | HELIX VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PROTEIN G |
| 3V3X | 2012-08-29 | 2.0 | Nitroxide Spin Labels in Protein GB1: N8/K28 Double Mutant |
| 1PGA | 1994-04-30 | 2.07 | TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON WITH NMR |
| 6WFW | 2020-07-29 | 2.09 | Crystal structure of Fab364 in complex with NPNA2 peptide from circumsporozoite protein |
| 5HI1 | 2016-02-24 | 2.15 | Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35 |
| 1UWX | 2005-06-15 | 2.2 | P1.2 serosubtype antigen derived from N. meningitidis PorA in complex with Fab fragment |
| 4OZA | 2014-07-16 | 2.2 | Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Gln32, beta-3-Asp36 |
| 5BMG | 2016-04-06 | 2.2 | Nitroxide Spin Labels in Protein GB1: E15 Mutant |
| 4WH4 | 2015-08-05 | 2.2 | Protein GB1 Quadruple Mutant I6H/N8H/K28H/Q32H |
| 6NLB | 2019-01-23 | 2.3 | Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-apo |
| 4OZC | 2014-07-16 | 2.3 | Backbone Modifications in the Protein GB1 Helix and Loops: beta-ACPC21, beta-ACPC24, beta-3-Lys28, beta-3-Lys31, beta-ACPC35, beta-ACPC40 |
| 6O41 | 2019-12-04 | 2.46 | Crystal structure of the unbound PGZL1 germline Fab fragment (PGZL1_gVmDmJ) |
| 1MVK | 2002-10-30 | 2.5 | X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G |
| 5BMI | 2016-04-06 | 2.5 | Nitroxide Spin Labels in Protein GB1: T44 Mutant, Crystal Form A |
| 1IGC | 1995-06-03 | 2.6 | IGG1 FAB FRAGMENT (MOPC21) COMPLEX WITH DOMAIN III OF PROTEIN G FROM STREPTOCOCCUS |
| 6U8C | 2019-10-23 | 2.61 | Crystal structure of an engineered ultra-high affinity Fab-Protein G complex |
| 6UUH | 2020-09-23 | 2.7 | Crystal structure of broad and potent HIV-1 neutralizing antibody 438-B11 |
| 3UI3 | 2012-02-08 | 2.8 | Structural and Biochemical Characterization of HP0315 from Helicobacter pylori as a VapD Protein with an Endoribonuclease Activity |
| 1FCC | 1995-04-20 | 3.2 | CRYSTAL STRUCTURE OF THE C2 FRAGMENT OF STREPTOCOCCAL PROTEIN G IN COMPLEX WITH THE FC DOMAIN OF HUMAN IGG |
| 6UYG | 2020-04-22 | 3.38 | Structure of Hepatitis C Virus Envelope Glycoprotein E2c3 core from genotype 6a bound to broadly neutralizing antibody AR3B and non neutralizing antibody E1 |
| 5LDE | 2017-10-04 | 3.38 | Crystal structure of a vFLIP-IKKgamma stapled peptide dimer |
| 6V9I | 2020-04-29 | 5.2 | cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2) |