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Crystal structure of RV0802C from mycobacterium tuberculosis in an unliganded form.

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

PDB: 2VZY
Type: protein
Length: 763 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RV0802C
UniProt: O06632
Ligands: ETX, SM, SO4
Pockets: 15 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RV0802C	protein	192	40% helix, 35% strand	O06632
B, D	RV0802C	protein	191	38% helix, 35% strand	O06632
C	RV0802C	protein	189	39% helix, 36% strand	O06632

Ligands and binding sites

ETX · 2-ethoxyethanol · ligand · 5 copies · chains A, B, C, D
SM · Samarium (III) ion · metal · chains D
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
FLC · Citrate anion · additive · 2 copies · chains B, D

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

Pockets

15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	80	0.75	0.98	22	empty
2	74	0.74	0.97	21	empty
3	274	0.52	0.75	41	empty
4	260	0.52	0.75	41	empty
5	161	0.44	0.75	26	ACT, SO4

Interfaces

4 interfaces between chains.

A–B · 1057 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1038 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 795 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 773 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2VZY · Crystal structure of Rv0802c from Mycobacterium tuberculosis in an unliganded 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 O06632
Elsewhere: RCSB PDB 2VZY · PDBe 2VZY · UniProt O06632

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