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Crystal structure of nitrosotalea devanaterra carotenoid cleavage dioxygenase in complex with 3-hydroxy-beta-apo-14'-carotenal

Analyse Crystal structure of nitrosotalea devanaterra carotenoid cleavage dioxygenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VCH
Type: protein
Length: 2,672 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carotenoid cleavage dioxygenase
UniProt: A0A128A3G4
Ligands: QVM, CO, NA, CL
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Carotenoid cleavage dioxygenase	protein	453	10% helix, 45% strand	A0A128A3G4
D	Carotenoid cleavage dioxygenase	protein	452	10% helix, 45% strand	A0A128A3G4
E	Carotenoid cleavage dioxygenase	protein	431	9% helix, 40% strand	A0A128A3G4
F	Carotenoid cleavage dioxygenase	protein	430	8% helix, 42% strand	A0A128A3G4

Ligands and binding sites

QVM · (2E,4E,6E,8E,10E)-11-[(4R)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-5,9-dimethylundeca-2,4,6, 8,10-pentaenal · ligand · 4 copies · chains A, B, C, D
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 A, 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	478	0.86	0.92	71	QVM
2	479	0.85	0.92	68	QVM
3	1066	0.84	0.85	129	QVM
4	781	0.84	0.86	107	QVM
5	1189	0.81	0.82	108	empty

Interfaces

8 interfaces between chains.

B–D · 1089 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1043 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 233 Å² buried · 1 hydrogen bond · protein-protein
E–F · 214 Å² buried · 1 hydrogen bond · protein-protein
B–E · 198 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6VCH · Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase in complex… · 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 6VCH · PDBe 6VCH · UniProt A0A128A3G4

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