MolNFT v1 · #70572 · protein
Crystal structure of mbti from mycobacterium tuberculosis
3LOG · Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti: “Crystal structure of mbti from mycobacterium tuberculosis”. X-ray diffraction, 2 ligands (NA, CO3), 20 pockets (best druggability 0.76). MolNFT v1 #70572 on GenesisL1: 3D…
- PDB
- 3LOG
- 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
- 5.4.4.2, 4.1.3.-
- UniProt
- Q7D785
- Ligands
- NA, CO3
- Pockets
- 20 · best druggability 0.76
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 5.4.4.2, 4.1.3.-) | protein | 435 | 33% helix, 35% strand | Q7D785 |
| B | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 5.4.4.2, 4.1.3.-) | protein | 450 | 31% helix, 36% strand | Q7D785 |
| D | Isochorismate SYNTHASE/ISOCHORISMATE-pyruvate lyase mbti (EC 5.4.4.2, 4.1.3.-) | protein | 440 | 32% helix, 35% strand | Q7D785 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- CO3 · Carbonate ion · ion · chains B
- SIN · Succinic acid · additive · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, 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 | 679 | 0.76 | 0.82 | 79 | GOL |
| 2 | 754 | 0.74 | 0.80 | 77 | empty |
| 3 | 153 | 0.74 | 0.92 | 40 | SIN |
| 4 | 222 | 0.73 | 0.88 | 42 | SIN, GOL |
| 5 | 63 | 0.73 | 0.98 | 23 | SIN, CO3 |
Interfaces
4 interfaces between chains.
- C–D · 782 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 667 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 595 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LOG · Crystal structure of MbtI from Mycobacterium tuberculosis · 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 3LOG · PDBe 3LOG · UniProt Q7D785
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