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Structure of a M. tuberculosis salicylate synthase, mbti, in complex with an inhibitor with ethyl R-group
Analyse Structure of a M. tuberculosis salicylate synthase, mbti, in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RV9
- Type
- protein
- Length
- 1,678 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
- RVD
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 4.1.3.-, 5.4.4.2) | protein | 420 | 32% helix, 34% strand | Q7D785 |
| B | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 4.1.3.-, 5.4.4.2) | protein | 420 | 31% helix, 33% strand | Q7D785 |
| C | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 4.1.3.-, 5.4.4.2) | protein | 413 | 33% helix, 34% strand | Q7D785 |
| D | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 4.1.3.-, 5.4.4.2) | protein | 425 | 31% helix, 32% strand | Q7D785 |
Ligands and binding sites
- RVD · 3-{[(1Z)-1-carboxybut-1-en-1-yl]oxy}-2-hydroxybenzoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.82 | 0.83 | 102 | empty |
| 2 | 621 | 0.79 | 0.84 | 79 | empty |
| 3 | 324 | 0.70 | 0.83 | 41 | RVD |
| 4 | 439 | 0.70 | 0.81 | 58 | RVD |
| 5 | 544 | 0.69 | 0.79 | 57 | RVD |
Interfaces
5 interfaces between chains.
- B–D · 705 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 421 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 361 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 299 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 187 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3RV9 · 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 3RV9 · PDBe 3RV9 · UniProt Q7D785
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