MolNFT v1 · #170027 · protein

Structure of coproheme decarboxylase from corynebacterium diphteriae in complex with monovinyl monopropionyl deuteroheme

6XUB · Chlorite dismutase: “Structure of coproheme decarboxylase from corynebacterium diphteriae in complex with monovinyl monopropionyl…”. X-ray diffraction, 1 ligand (VOV), 20 pockets (best druggability 0.77). MolNFT v1 #170027 on…

PDB: 6XUB
Type: protein
Length: 1,142 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chlorite dismutase
UniProt: A0A2T1BSE4
Ligands: VOV
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Chlorite dismutase	protein	230	33% helix, 28% strand	A0A2T1BSE4
B	Chlorite dismutase	protein	231	33% helix, 28% strand	A0A2T1BSE4
D	Chlorite dismutase	protein	228	32% helix, 28% strand	A0A2T1BSE4
E	Chlorite dismutase	protein	223	31% helix, 29% strand	A0A2T1BSE4

Ligands and binding sites

VOV · harderoheme (III) · ligand · 5 copies · chains A, B, C, D, 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	541	0.77	0.84	52	VOV
2	504	0.76	0.84	53	VOV
3	498	0.76	0.84	51	VOV
4	539	0.75	0.83	51	VOV
5	511	0.74	0.82	48	VOV

Interfaces

5 interfaces between chains.

A–C · 1534 Å² buried · 23 hydrogen bonds · protein-protein
D–E · 1496 Å² buried · 19 hydrogen bonds · protein-protein
B–E · 1487 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1487 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1483 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

6XUB · Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with… · 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 A0A2T1BSE4
Elsewhere: RCSB PDB 6XUB · PDBe 6XUB · UniProt A0A2T1BSE4

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