MolNFT v1 · #32389 · protein

Crystal structure of 3-chlorocatechol 1,2-dioxygenase from rhodococcus opacus 1CP

2BOY: “Crystal structure of 3-chlorocatechol 1,2-dioxygenase from rhodococcus opacus 1CP”. X-ray diffraction, 4 ligands (BHO, LPP, MG), 17 pockets (best druggability 0.85). MolNFT v1 #32389 on GenesisL1: 3D structure, binding sites and…

PDB: 2BOY
Type: protein
Length: 2,003 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-chlorocatechol 1,2-dioxygenase
EC: 1.13.11.1
UniProt: Q8G9L3
Ligands: BHO, LPP, MG, FE
Pockets: 17 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 27% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-chlorocatechol 1,2-dioxygenase (EC 1.13.11.1)	protein	253	26% helix, 26% strand	Q8G9L3
B	3-chlorocatechol 1,2-dioxygenase (EC 1.13.11.1)	protein	252	27% helix, 27% strand	Q8G9L3
C, D	3-chlorocatechol 1,2-dioxygenase (EC 1.13.11.1)	protein	251	26% helix, 26% strand	Q8G9L3
E, G	3-chlorocatechol 1,2-dioxygenase (EC 1.13.11.1)	protein	250	27% helix, 26% strand	Q8G9L3
F, H	3-chlorocatechol 1,2-dioxygenase (EC 1.13.11.1)	protein	248	27% helix, 25% strand	Q8G9L3

Ligands and binding sites

BHO · Benzhydroxamic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
LPP · 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate · ligand · 8 copies · chains A, B, H, C, D, E, F, G
MG · Magnesium ion · metal · 16 copies · chains A, B, G, C, F, D, E, H
FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	687	0.85	0.88	48	LPP
2	50	0.72	0.99	17	BHO
3	547	0.65	0.77	78	MG
4	462	0.64	0.77	53	empty
5	484	0.62	0.76	79	MG

Interfaces

11 interfaces between chains.

D–H · 2406 Å² buried · 25 hydrogen bonds · protein-protein
C–F · 540 Å² buried · 1 hydrogen bond · protein-protein
B–G · 518 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 443 Å² buried · 4 hydrogen bonds · protein-protein
B–H · 159 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2BOY · Crystal structure of 3-ChloroCatechol 1,2-Dioxygenase from Rhodococcus Opacus 1CP · 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 Q8G9L3
Elsewhere: RCSB PDB 2BOY · PDBe 2BOY · UniProt Q8G9L3

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