MolNFT v1 · #167160 · protein

Crystal structure of nitrosotalea devanaterra carotenoid cleavage dioxygenase, iron form

6VCF: “Crystal structure of nitrosotalea devanaterra carotenoid cleavage dioxygenase, iron form”. X-ray diffraction, 4 ligands (BCT, FE2, NA), 20 pockets (best druggability 0.85). MolNFT v1 #167160 on GenesisL1: 3D structure, binding sites…

PDB: 6VCF
Type: protein
Length: 2,679 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carotenoid cleavage dioxygenase
UniProt: A0A128A3G4
Ligands: BCT, FE2, NA, CL
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 9% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Carotenoid cleavage dioxygenase	protein	453	9% helix, 44% strand	A0A128A3G4
B	Carotenoid cleavage dioxygenase	protein	455	9% helix, 43% strand	A0A128A3G4
D	Carotenoid cleavage dioxygenase	protein	452	9% helix, 43% strand	A0A128A3G4
E	Carotenoid cleavage dioxygenase	protein	432	9% helix, 38% strand	A0A128A3G4
F	Carotenoid cleavage dioxygenase	protein	434	8% helix, 42% strand	A0A128A3G4

Ligands and binding sites

BCT · Bicarbonate ion · ligand · 2 copies · chains B, C
FE2 · Fe (II) ion · metal · 6 copies · chains A, B, C, D, E, F
NA · Sodium ion · metal · 2 copies · chains A, C, B, D
CL · Chloride ion · ion · chains A

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	377	0.85	0.93	62	empty
2	1128	0.85	0.85	115	empty
3	570	0.84	0.89	88	BCT
4	591	0.84	0.89	89	BCT
5	303	0.82	0.92	53	empty

Interfaces

9 interfaces between chains.

A–C · 1111 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 1076 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 284 Å² buried · 1 hydrogen bond · protein-protein
A–B · 279 Å² buried · 1 hydrogen bond · protein-protein
B–E · 227 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6VCF · Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase, iron form · 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 A0A128A3G4
Elsewhere: RCSB PDB 6VCF · PDBe 6VCF · UniProt A0A128A3G4

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