MolNFT v1 · #3325 · protein
The monofunctional chorismate mutase from bacillus subtilis: structure determination of chorismate mutase and its complexes with a transition state analog and prephenate, and implications on the mechanism of enzymatic reaction
1COM: “The monofunctional chorismate mutase from bacillus subtilis: structure determination of chorismate mutase and…”. X-ray diffraction, 1 ligand (PRE), 15 pockets (best druggability 0.65). MolNFT v1 #3325 on GenesisL1: 3D structure…
- PDB
- 1COM
- Type
- protein
- Length
- 1,386 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chorismate mutase
- EC
- 5.4.99.5
- UniProt
- P19080
- Ligands
- PRE
- Pockets
- 15 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, H, I, J, L | Chorismate mutase (EC 5.4.99.5) | protein | 114 | 32% helix, 29% strand | P19080 |
| B, E | Chorismate mutase (EC 5.4.99.5) | protein | 118 | 31% helix, 28% strand | P19080 |
| C | Chorismate mutase (EC 5.4.99.5) | protein | 119 | 31% helix, 28% strand | P19080 |
| F | Chorismate mutase (EC 5.4.99.5) | protein | 117 | 34% helix, 28% strand | P19080 |
| K | Chorismate mutase (EC 5.4.99.5) | protein | 116 | 29% helix, 28% strand | P19080 |
Ligands and binding sites
- PRE · Prephenic acid · ligand · 9 copies · chains A, C, B, D, F, E, G, I, H, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.65 | 0.81 | 30 | PRE |
| 2 | 189 | 0.62 | 0.83 | 24 | PRE |
| 3 | 152 | 0.60 | 0.84 | 18 | PRE |
| 4 | 197 | 0.59 | 0.81 | 25 | PRE |
| 5 | 218 | 0.58 | 0.80 | 27 | empty |
Interfaces
14 interfaces between chains.
- B–C · 1189 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1184 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1147 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1141 Ų buried · 15 hydrogen bonds · protein-protein
- J–K · 1128 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1COM · The monofunctional chorismate mutase from bacillus subtilis: structure determination of… · the same entry in another collection · chain L against L, 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 P19080
- Elsewhere: RCSB PDB 1COM · PDBe 1COM · UniProt P19080
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