MolNFT v1 · #113427 · protein

X-ray crystal structure of RV2018 from mycobacterium tuberculosis

5AF3 · VAPBC49: “X-ray crystal structure of RV2018 from mycobacterium tuberculosis”. X-ray diffraction, 4 pockets (best druggability 0.67). MolNFT v1 #113427 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AF3
Type: protein
Length: 428 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VAPBC49
UniProt: O53464
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VAPBC49	protein	214	51% helix, 14% strand	O53464
B	VAPBC49	protein	214	52% helix, 14% strand	O53464

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	645	0.67	0.76	55	empty
2	79	0.42	0.80	21	empty
3	60	0.35	0.78	15	empty
4	57	0.35	0.78	14	empty

Interfaces

1 interface between chains.

A–B · 1003 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5AF3 · X-ray crystal structure of RV2018 from mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
O53464 · AlphaFold monomer V2.0 prediction for putative antitoxin VAPB45 (O53464) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 O53464
Elsewhere: RCSB PDB 5AF3 · PDBe 5AF3 · UniProt O53464

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