MolNFT v1 · #81820 · protein

Nitroxide spin labels in protein GB1: N8/K28 double mutant

3V3X · Immunoglobulin G-binding protein G: “Nitroxide spin labels in protein GB1: N8/K28 double mutant”. X-ray diffraction, 1 ligand (MTN), 1 pocket (best druggability 0.43). MolNFT v1 #81820 on GenesisL1: 3D structure, binding sites and…

PDB: 3V3X
Type: protein
Length: 224 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin G-binding protein G
UniProt: P19909
Ligands: MTN
Pockets: 1 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Immunoglobulin G-binding protein G	protein	56	23% helix, 50% strand	P19909

Ligands and binding sites

MTN · S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate · ligand · 7 copies · chains A, C, B, D
ACT · Acetate ion · additive · 2 copies · chains B, D
2PE · Nonaethylene glycol · additive · chains A, B, D
GOL · Glycerol · additive · chains B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	177	0.43	0.74	21	empty

Interfaces

5 interfaces between chains.

A–C · 1891 Å² buried · 47 hydrogen bonds · protein-protein
B–D · 1888 Å² buried · 56 hydrogen bonds · protein-protein
A–D · 340 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 60 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 38 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 covalent (covalent ligand).

Compared structures

3V3X · Nitroxide Spin Labels in Protein GB1: N8/K28 Double Mutant · the same entry in another collection · chain A against A, TM-score 1.00
P19909 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein G (P19909) · a predicted model of the same protein · chain A against A, TM-score 0.73

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P19909
Elsewhere: RCSB PDB 3V3X · PDBe 3V3X · UniProt P19909

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