Research workbench
ARG90CIT chorismate mutase of bacillus subtilis in complex with a transition state analog
Analyse ARG90CIT chorismate mutase of bacillus subtilis in complex with a transition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZP4
- Type
- protein
- Length
- 696 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chorismate mutase aroh
- UniProt
- P19080
- Ligands
- CIR, TSA
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Chorismate mutase aroh | protein | 116 | 33% helix, 27% strand | P19080 |
Ligands and binding sites
- CIR · Citrulline · ligand · 6 copies · chains A, C, B, D, F, E
- TSA · 8-hydroxy-2-oxa-bicyclo[3.3.1]non-6-ene-3,5-dicarboxylic acid · ligand · 4 copies · chains B, C, A, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.80 | 0.81 | 112 | CIR, TSA |
| 2 | 259 | 0.69 | 0.84 | 33 | CIR, TSA |
| 3 | 287 | 0.68 | 0.83 | 44 | CIR |
| 4 | 316 | 0.68 | 0.82 | 39 | CIR, TSA |
| 5 | 350 | 0.65 | 0.80 | 43 | CIR |
Interfaces
10 interfaces between chains.
- E–F · 1103 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1088 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1071 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1032 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1022 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 3ZP4 · Arg90Cit chorismate mutase of Bacillus subtilis in complex with a transition state analog · the same entry in another collection · chain C against C, TM-score 1.00
- P19080 · AlphaFold monomer V2.0 prediction for chorismate mutase aroh (P19080) · a predicted model of the same protein · chain A 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 P19080
- Elsewhere: RCSB PDB 3ZP4 · PDBe 3ZP4 · UniProt P19080
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