MolNFT v1 · #73654 · protein
Crystal structure of 2-methylcitrate synthase (prpc) from salmonella typhimurium
3O8J: “Crystal structure of 2-methylcitrate synthase (prpc) from salmonella typhimurium”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #73654 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3O8J
- Type
- protein
- Length
- 3,624 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-methylcitrate synthase
- EC
- 2.3.3.5
- UniProt
- Q56063
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, G | 2-methylcitrate synthase (EC 2.3.3.5) | protein | 364 | 59% helix, 4% strand | Q56063 |
| C | 2-methylcitrate synthase (EC 2.3.3.5) | protein | 360 | 60% helix, 4% strand | Q56063 |
| D | 2-methylcitrate synthase (EC 2.3.3.5) | protein | 358 | 62% helix, 4% strand | Q56063 |
| H, I | 2-methylcitrate synthase (EC 2.3.3.5) | protein | 362 | 62% helix, 4% strand | Q56063 |
| J | 2-methylcitrate synthase (EC 2.3.3.5) | protein | 362 | 61% helix, 4% strand | Q56063 |
Ligands and binding sites
- GOL · Glycerol · additive · 11 copies · chains A, B, C, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.85 | 0.86 | 109 | empty |
| 2 | 1170 | 0.82 | 0.83 | 133 | empty |
| 3 | 387 | 0.80 | 0.89 | 52 | empty |
| 4 | 504 | 0.79 | 0.86 | 72 | empty |
| 5 | 871 | 0.78 | 0.81 | 91 | GOL |
Interfaces
25 interfaces between chains.
- A–B · 3495 Ų buried · 53 hydrogen bonds · protein-protein
- E–F · 3441 Ų buried · 52 hydrogen bonds · protein-protein
- G–H · 3393 Ų buried · 59 hydrogen bonds · protein-protein
- I–J · 3365 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 3315 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 3O8J · Crystal structure of 2-methylcitrate synthase (PrpC) from Salmonella typhimurium · the same entry in another collection · chain D against D, TM-score 1.00
- Q56063 · AlphaFold monomer V2.0 prediction for 2-methylcitrate synthase (Q56063) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q56063
- Elsewhere: RCSB PDB 3O8J · PDBe 3O8J · UniProt Q56063
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