MolNFT v1 · #77989 · protein
Structure of a M. tuberculosis salicylate synthase, mbti, in complex with an inhibitor with cyclopropyl R-group
3RV8 · Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti: “Structure of a M. tuberculosis salicylate synthase, mbti, in complex with an inhibitor with cyclopropyl…”. X-ray diffraction, 2 ligands (RVC, VCE), 20 pockets (best…
- PDB
- 3RV8
- Type
- protein
- Length
- 1,700 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
- RVC, VCE
- Pockets
- 20 · best druggability 0.79
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 | 418 | 33% helix, 32% strand | Q7D785 |
| B | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 4.1.3.-, 5.4.4.2) | protein | 432 | 32% helix, 32% strand | Q7D785 |
| C | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 4.1.3.-, 5.4.4.2) | protein | 430 | 33% helix, 33% strand | Q7D785 |
| D | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 4.1.3.-, 5.4.4.2) | protein | 420 | 31% helix, 33% strand | Q7D785 |
Ligands and binding sites
- RVC · 3-{[(Z)-1-carboxy-2-cyclopropylethenyl]oxy}-2-hydroxybenzoic acid · ligand · 4 copies · chains A, B, C, D
- VCE · 3-{[(E)-1-carboxy-2-cyclopropylethenyl]oxy}-2-hydroxybenzoic acid · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.79 | 0.82 | 86 | empty |
| 2 | 741 | 0.78 | 0.83 | 75 | empty |
| 3 | 1070 | 0.77 | 0.79 | 103 | RVC |
| 4 | 533 | 0.74 | 0.82 | 65 | RVC, VCE |
| 5 | 561 | 0.71 | 0.79 | 78 | empty |
Interfaces
4 interfaces between chains.
- C–D · 678 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 653 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 524 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 473 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3RV8 · 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 3RV8 · PDBe 3RV8 · UniProt Q7D785
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