Research workbench
M. tuberculosis salicylate synthase mbti in complex with salicylate and MG2+
Analyse M. tuberculosis salicylate synthase mbti in complex with salicylate and MG2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZA5
- Type
- protein
- Length
- 1,756 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
- SAL, MG, SO4
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 34% 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 | 445 | 32% helix, 34% strand | P9WFX1 |
| B | Salicylate synthase (EC 5.4.99.5, 4.2.99.21, 5.4.4.2) | protein | 440 | 32% helix, 35% strand | P9WFX1 |
| C | Salicylate synthase (EC 5.4.99.5, 4.2.99.21, 5.4.4.2) | protein | 435 | 32% helix, 34% strand | P9WFX1 |
| D | Salicylate synthase (EC 5.4.99.5, 4.2.99.21, 5.4.4.2) | protein | 436 | 32% helix, 35% strand | P9WFX1 |
Ligands and binding sites
- SAL · 2-hydroxybenzoic acid · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 34 copies · chains A, C, B, D
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.85 | 0.86 | 97 | MG |
| 2 | 932 | 0.77 | 0.79 | 88 | empty |
| 3 | 75 | 0.76 | 0.99 | 28 | SAL, SO4 |
| 4 | 553 | 0.75 | 0.82 | 61 | SO4 |
| 5 | 56 | 0.72 | 0.98 | 24 | SAL, SO4 |
Interfaces
4 interfaces between chains.
- A–C · 726 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 595 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 518 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 133 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZA5 · M. tuberculosis salicylate synthase MbtI in complex with salicylate and Mg2+ · 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 D 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 6ZA5 · PDBe 6ZA5 · UniProt P9WFX1
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