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Crystal structure of RV0802C from mycobacterium tuberculosis in complex with succinyl-CoA

Analyse Crystal structure of RV0802C from mycobacterium tuberculosis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VZZ
Type: protein
Length: 840 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RV0802C
UniProt: O06632
Ligands: SCA
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RV0802C	protein	210	38% helix, 32% strand	O06632

Ligands and binding sites

SCA · Succinyl-coenzyme A · ligand · 4 copies · chains A, B, C, D

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	666	0.74	0.80	80	SCA
2	63	0.73	0.98	21	empty
3	64	0.72	0.98	21	empty
4	470	0.72	0.82	54	SCA
5	461	0.72	0.82	50	SCA

Interfaces

4 interfaces between chains.

B–D · 1085 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1066 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 760 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 757 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2VZZ · Crystal structure of Rv0802c from Mycobacterium tuberculosis in Complex with Succinyl-CoA · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O06632
Elsewhere: RCSB PDB 2VZZ · PDBe 2VZZ · UniProt O06632

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