MolNFT v1 · #82170 · protein
Structure of a M. tuberculosis salicylate synthase, mbti, in complex with an inhibitor methylamt
3VEH · Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti: “Structure of a M. tuberculosis salicylate synthase, mbti, in complex with an inhibitor methylamt”. X-ray diffraction, 3 ligands (0GA, K, SCN), 20 pockets (best druggability…
- PDB
- 3VEH
- Type
- protein
- Length
- 1,760 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti
- EC
- 4.1.3.-, 5.4.4.2
- UniProt
- Q7D785
- Ligands
- 0GA, K, SCN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 4.1.3.-, 5.4.4.2) | protein | 435 | 33% helix, 35% strand | Q7D785 |
| B | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 4.1.3.-, 5.4.4.2) | protein | 451 | 31% helix, 36% strand | Q7D785 |
| D | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 4.1.3.-, 5.4.4.2) | protein | 439 | 32% helix, 34% strand | Q7D785 |
Ligands and binding sites
- 0GA · 3-{[(1Z)-1-carboxyprop-1-en-1-yl]oxy}-2-hydroxybenzoic acid · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 2 copies · chains A, B, D
- SCN · Thiocyanate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.77 | 0.82 | 79 | K |
| 2 | 335 | 0.76 | 0.87 | 45 | 0GA |
| 3 | 405 | 0.76 | 0.86 | 46 | 0GA |
| 4 | 251 | 0.76 | 0.89 | 35 | 0GA |
| 5 | 752 | 0.74 | 0.80 | 79 | PEG, K |
Interfaces
4 interfaces between chains.
- C–D · 690 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 665 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 585 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 95 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3VEH · Structure of a M. tuberculosis salicylate synthase, MbtI, in complex with an inhibitor… · 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 Q7D785
- Elsewhere: RCSB PDB 3VEH · PDBe 3VEH · UniProt Q7D785
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