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Structure of putative oxidoreductase yvaa from bacillus subtilis in triclinic form

Analyse Structure of putative oxidoreductase yvaa from bacillus subtilis in triclinic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GFG
Type: protein
Length: 4,081 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized oxidoreductase yvaa
UniProt: O32223
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 12 distinct chains · 37% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized oxidoreductase yvaa	protein	340	37% helix, 24% strand	O32223
B	Uncharacterized oxidoreductase yvaa	protein	350	37% helix, 23% strand	O32223
C	Uncharacterized oxidoreductase yvaa	protein	346	36% helix, 24% strand	O32223
D	Uncharacterized oxidoreductase yvaa	protein	335	37% helix, 25% strand	O32223
E	Uncharacterized oxidoreductase yvaa	protein	342	37% helix, 23% strand	O32223
F	Uncharacterized oxidoreductase yvaa	protein	342	37% helix, 24% strand	O32223
G	Uncharacterized oxidoreductase yvaa	protein	340	36% helix, 26% strand	O32223
H	Uncharacterized oxidoreductase yvaa	protein	339	37% helix, 24% strand	O32223
I	Uncharacterized oxidoreductase yvaa	protein	336	37% helix, 24% strand	O32223
J	Uncharacterized oxidoreductase yvaa	protein	340	37% helix, 24% strand	O32223
K	Uncharacterized oxidoreductase yvaa	protein	337	38% helix, 25% strand	O32223
L	Uncharacterized oxidoreductase yvaa	protein	334	37% helix, 25% strand	O32223

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	1059	0.76	0.78	125	empty
2	130	0.72	0.93	31	empty
3	108	0.72	0.94	35	empty
4	108	0.72	0.94	34	empty
5	128	0.71	0.92	32	empty

Interfaces

17 interfaces between chains.

G–H · 1644 Å² buried · 25 hydrogen bonds · protein-protein
I–J · 1643 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1632 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1630 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 1629 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

3GFG · Structure of putative oxidoreductase yvaA from Bacillus subtilis in triclinic form · the same entry in another collection · chain L against L, 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 O32223
Elsewhere: RCSB PDB 3GFG · PDBe 3GFG · UniProt O32223

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