MolNFT v1 · #171589 · protein

M. tuberculosis salicylate synthase mbti in complex with BA2+

6ZA6: “M. tuberculosis salicylate synthase mbti in complex with BA2+”. X-ray diffraction, 3 ligands (BA, CL, PO4), 18 pockets (best druggability 0.75). MolNFT v1 #171589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZA6
Type: protein
Length: 1,758 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Salicylate synthase
EC: 5.4.99.5, 4.2.99.21, 5.4.4.2
UniProt: P9WFX1
Ligands: BA, CL, PO4
Pockets: 18 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Salicylate synthase (EC 5.4.99.5, 4.2.99.21, 5.4.4.2)	protein	435	33% helix, 35% strand	P9WFX1
B	Salicylate synthase (EC 5.4.99.5, 4.2.99.21, 5.4.4.2)	protein	451	31% helix, 36% strand	P9WFX1
C	Salicylate synthase (EC 5.4.99.5, 4.2.99.21, 5.4.4.2)	protein	435	33% helix, 35% strand	P9WFX1
D	Salicylate synthase (EC 5.4.99.5, 4.2.99.21, 5.4.4.2)	protein	437	33% helix, 35% strand	P9WFX1

Ligands and binding sites

BA · Barium ion · metal · 2 copies · chains B, D
CL · Chloride ion · ion · 5 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 4 copies · chains A, B, C, D

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

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1008	0.75	0.77	108	GOL
2	61	0.72	0.98	27	PO4, CL
3	172	0.69	0.88	35	PO4, CL
4	139	0.69	0.89	31	PO4, CL
5	414	0.64	0.78	56	empty

Interfaces

4 interfaces between chains.

A–D · 675 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 571 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 359 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 332 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6ZA6 · M. tuberculosis salicylate synthase MbtI in complex with Ba2+ · the same entry in another collection · chain D against D, TM-score 1.00
P9WFX1 · AlphaFold monomer V2.0 prediction for salicylate synthase (P9WFX1) · a predicted model of the same protein · chain C 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 P9WFX1
Elsewhere: RCSB PDB 6ZA6 · PDBe 6ZA6 · UniProt P9WFX1

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