Research workbench
Crystal structure of methylcitrate synthase from mycobacterium tuberculosis
Analyse Crystal structure of methylcitrate synthase from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HWK
- Type
- protein
- Length
- 2,920 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylcitrate synthase
- EC
- 2.3.3.1
- UniProt
- O08395
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylcitrate synthase (EC 2.3.3.1) | protein | 366 | 60% helix, 6% strand | O08395 |
| B, C, G | Methylcitrate synthase (EC 2.3.3.1) | protein | 364 | 59% helix, 6% strand | O08395 |
| D, F, H | Methylcitrate synthase (EC 2.3.3.1) | protein | 365 | 61% helix, 6% strand | O08395 |
| E | Methylcitrate synthase (EC 2.3.3.1) | protein | 367 | 60% helix, 6% strand | O08395 |
Ligands and binding sites
- SIN · Succinic acid · additive · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.83 | 0.85 | 79 | SIN |
| 2 | 832 | 0.82 | 0.85 | 75 | SIN |
| 3 | 711 | 0.81 | 0.85 | 78 | empty |
| 4 | 795 | 0.81 | 0.84 | 99 | empty |
| 5 | 197 | 0.72 | 0.89 | 26 | SIN |
Interfaces
19 interfaces between chains.
- C–D · 4356 Ų buried · 93 hydrogen bonds · protein-protein
- E–F · 4344 Ų buried · 90 hydrogen bonds · protein-protein
- A–B · 4328 Ų buried · 87 hydrogen bonds · protein-protein
- G–H · 4319 Ų buried · 92 hydrogen bonds · protein-protein
- C–E · 996 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3HWK · Crystal structure of methylcitrate synthase 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 O08395
- Elsewhere: RCSB PDB 3HWK · PDBe 3HWK · UniProt O08395
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