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Anbu (gly-1) mutant from hyphomicrobium sp. strain MC1 - sg P2(1)2(1) 2(1)

Analyse Anbu (gly-1) mutant from hyphomicrobium sp. strain MC1 - sg P2(1)2(1) 2(1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NYG
Type: protein
Length: 1,843 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anbu
UniProt: F8JB59
Pockets: 18 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 34% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Anbu	protein	235	33% helix, 28% strand	F8JB59
B, C, D, H	Anbu	protein	231	35% helix, 28% strand	F8JB59
E	Anbu	protein	227	36% helix, 29% strand	F8JB59
F	Anbu	protein	229	34% helix, 29% strand	F8JB59
G	Anbu	protein	228	34% helix, 29% strand	F8JB59

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains B, C, D, F, A, E, H

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

Pockets

18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1075	0.85	0.86	121	empty
2	1163	0.82	0.83	100	empty
3	70	0.74	0.98	17	TRS
4	633	0.74	0.81	79	empty
5	59	0.73	0.99	17	TRS

Interfaces

11 interfaces between chains.

B–C · 2186 Å² buried · 31 hydrogen bonds · protein-protein
D–F · 2158 Å² buried · 31 hydrogen bonds · protein-protein
A–E · 1868 Å² buried · 23 hydrogen bonds · protein-protein
F–G · 767 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 763 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5NYG · Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 - SG P2(1)2(1)2(1) · the same entry in another collection · chain A against A, TM-score 1.00

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 F8JB59
Elsewhere: RCSB PDB 5NYG · PDBe 5NYG · UniProt F8JB59

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