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Crystal structure of ovob

Analyse Crystal structure of ovob in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Z0Q
Type: protein
Length: 4,526 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminotransferase, class I and II
UniProt: B2VJB8
Ligands: PLP
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, B, F, G	Aminotransferase, class I and II	protein	379	39% helix, 16% strand	B2VJB8
A, K	Aminotransferase, class I and II	protein	376	40% helix, 18% strand	B2VJB8
D, E	Aminotransferase, class I and II	protein	378	43% helix, 16% strand	B2VJB8
H	Aminotransferase, class I and II	protein	378	37% helix, 17% strand	B2VJB8
I, J	Aminotransferase, class I and II	protein	375	39% helix, 17% strand	B2VJB8
L	Aminotransferase, class I and II	protein	374	39% helix, 16% strand	B2VJB8

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 12 copies · chains C, E, A, I, B, K, D, G, F, J, H, L

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	1052	0.81	0.82	130	PLP
2	1151	0.79	0.81	136	PLP
3	1183	0.79	0.80	128	PLP
4	1121	0.79	0.80	118	PLP
5	1193	0.78	0.80	122	PLP

Interfaces

20 interfaces between chains.

F–J · 2459 Å² buried · 38 hydrogen bonds · protein-protein
C–E · 2435 Å² buried · 33 hydrogen bonds · protein-protein
D–G · 2414 Å² buried · 36 hydrogen bonds · protein-protein
A–I · 2386 Å² buried · 43 hydrogen bonds · protein-protein
B–K · 2344 Å² buried · 35 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 cofactor (pyridoxal phosphate Schiff base).

Compared structures

5Z0Q · Crystal Structure of OvoB · the same entry in another collection · chain C against C, 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 B2VJB8
Elsewhere: RCSB PDB 5Z0Q · PDBe 5Z0Q · UniProt B2VJB8

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