MolNFT v1 · #144074 · protein

Crystal structure of cobalt-substituted synechocystis aco

6BIG · Apocarotenoid-15,15'-oxygenase: “Crystal structure of cobalt-substituted synechocystis aco”. X-ray diffraction, 2 ligands (CO, CL), 20 pockets (best druggability 0.87). MolNFT v1 #144074 on GenesisL1: 3D structure, binding sites and…

PDB: 6BIG
Type: protein
Length: 1,916 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apocarotenoid-15,15'-oxygenase
EC: 1.13.11.75
UniProt: P74334
Ligands: CO, CL
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Apocarotenoid-15,15'-oxygenase (EC 1.13.11.75)	protein	479	9% helix, 41% strand	P74334

Ligands and binding sites

CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 3 copies · chains A, C, B, D

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

Pockets

20 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	975	0.87	0.88	101	CL
2	1080	0.86	0.87	91	empty
3	1141	0.86	0.87	100	empty
4	1154	0.85	0.86	85	empty
5	432	0.79	0.87	40	empty

Interfaces

3 interfaces between chains.

A–C · 594 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 539 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 534 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6BIG · Crystal structure of cobalt-substituted Synechocystis ACO · the same entry in another collection · chain D against D, TM-score 1.00
P74334 · AlphaFold monomer V2.0 prediction for apocarotenoid-15,15'-oxygenase (P74334) · a predicted model of the same protein · chain B 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 P74334
Elsewhere: RCSB PDB 6BIG · PDBe 6BIG · UniProt P74334

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