MolNFT v1 · #167500 · protein

Crystal structure of the H767A mutant of goxa soaked with glycine

6VMV · Glycine oxidase: “Crystal structure of the H767A mutant of goxa soaked with glycine”. X-ray diffraction, 2 ligands (MG, SO4), 20 pockets (best druggability 0.85). MolNFT v1 #167500 on GenesisL1: 3D structure, binding sites and…

PDB: 6VMV
Type: protein
Length: 3,090 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycine oxidase
UniProt: A0A161XU12
Ligands: MG, SO4
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycine oxidase	protein	765	32% helix, 21% strand	A0A161XU12
B	Glycine oxidase	protein	778	31% helix, 20% strand	A0A161XU12
C	Glycine oxidase	protein	769	32% helix, 21% strand	A0A161XU12
D	Glycine oxidase	protein	778	32% helix, 21% strand	A0A161XU12

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 9 copies · chains A, D, B, C

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	485	0.85	0.92	55	empty
2	474	0.84	0.91	53	empty
3	1144	0.81	0.83	127	empty
4	732	0.79	0.83	93	empty
5	143	0.76	0.94	24	empty

Interfaces

6 interfaces between chains.

B–C · 2941 Å² buried · 54 hydrogen bonds · protein-protein
A–D · 2935 Å² buried · 63 hydrogen bonds · protein-protein
A–B · 2151 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2130 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 256 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

6VMV · Crystal structure of the H767A mutant of GoxA soaked with glycine · 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 A0A161XU12
Elsewhere: RCSB PDB 6VMV · PDBe 6VMV · UniProt A0A161XU12

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