MolNFT v1 · #114337 · protein

Nitroxide spin labels in protein GB1: E15 mutant

5BMG · Immunoglobulin G-binding protein G: “Nitroxide spin labels in protein GB1: E15 mutant”. X-ray diffraction, 1 ligand (MTN), 7 pockets (best druggability 0.81). MolNFT v1 #114337 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5BMG
Type: protein
Length: 448 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin G-binding protein G
UniProt: P19909
Ligands: MTN
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Immunoglobulin G-binding protein G	protein	56	25% helix, 43% 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, G, H, B, C, D, E, F
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B, F

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1000	0.81	0.82	72	MTN
2	979	0.80	0.81	81	MTN
3	166	0.50	0.78	21	empty
4	86	0.42	0.79	22	empty
5	104	0.39	0.76	14	empty

Interfaces

14 interfaces between chains.

E–F · 379 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 364 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 332 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 328 Å² buried · 10 hydrogen bonds · protein-protein
A–G · 278 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5BMG · Nitroxide Spin Labels in Protein GB1: E15 Mutant · the same entry in another collection · chain H against H, 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 0.97

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 5BMG · PDBe 5BMG · UniProt P19909

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