MolNFT v1 · #167161 · protein

Crystal structure of nitrosotalea devanaterra carotenoid cleavage dioxygenase, cobalt form

6VCG: “Crystal structure of nitrosotalea devanaterra carotenoid cleavage dioxygenase, cobalt form”. X-ray diffraction, 3 ligands (CO, NA, CL), 20 pockets (best druggability 0.85). MolNFT v1 #167161 on GenesisL1: 3D structure, binding sites…

PDB: 6VCG
Type: protein
Length: 2,665 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carotenoid cleavage dioxygenase
UniProt: A0A128A3G4
Ligands: CO, NA, CL
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Carotenoid cleavage dioxygenase	protein	453	10% helix, 44% strand	A0A128A3G4
D	Carotenoid cleavage dioxygenase	protein	453	10% helix, 45% strand	A0A128A3G4
E	Carotenoid cleavage dioxygenase	protein	423	9% helix, 39% strand	A0A128A3G4
F	Carotenoid cleavage dioxygenase	protein	430	8% helix, 42% strand	A0A128A3G4

Ligands and binding sites

CO · Cobalt (II) ion · metal · 6 copies · chains A, B, C, D, E, F
NA · Sodium ion · metal · 2 copies · chains B, D, A, C
CL · Chloride ion · ion · 2 copies · chains C, E

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	1027	0.85	0.85	127	empty
2	418	0.84	0.92	67	empty
3	404	0.84	0.92	67	empty
4	815	0.83	0.85	118	empty
5	834	0.81	0.84	116	empty

Interfaces

6 interfaces between chains.

B–D · 1094 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 1043 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 217 Å² buried · 1 hydrogen bond · protein-protein
B–E · 198 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 180 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6VCG · Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase, cobalt 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 6VCG · PDBe 6VCG · UniProt A0A128A3G4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.