Research workbench
Crystal structure of aminohydrolase from caulobacter crescentus
Analyse Crystal structure of aminohydrolase from caulobacter crescentus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RAG
- Type
- protein
- Length
- 1,476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidase
- UniProt
- Q9A4T4
- Ligands
- ZN, CL
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dipeptidase | protein | 369 | 45% helix, 15% strand | Q9A4T4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.70 | 0.80 | 62 | empty |
| 2 | 386 | 0.56 | 0.74 | 53 | ZN, CL |
| 3 | 194 | 0.54 | 0.79 | 25 | empty |
| 4 | 310 | 0.54 | 0.75 | 25 | empty |
| 5 | 347 | 0.54 | 0.74 | 50 | ZN, CL |
Interfaces
4 interfaces between chains.
- A–B · 813 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 799 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 627 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 602 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2RAG · Crystal structure of aminohydrolase from Caulobacter crescentus · 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 Q9A4T4
- Elsewhere: RCSB PDB 2RAG · PDBe 2RAG · UniProt Q9A4T4
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