MolNFT v1 · #138830 · protein
Crystal structure of carboxypeptidase from thermus thermophilus
5WVU · Thermostable carboxypeptidase 1: “Crystal structure of carboxypeptidase from thermus thermophilus”. X-ray diffraction, 1 ligand (ZN), 15 pockets (best druggability 0.83). MolNFT v1 #138830 on GenesisL1: 3D structure, binding sites…
- PDB
- 5WVU
- Type
- protein
- Length
- 1,530 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermostable carboxypeptidase 1
- EC
- 3.4.17.19
- UniProt
- Q5SLM3
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Thermostable carboxypeptidase 1 (EC 3.4.17.19) | protein | 510 | 67% helix, 3% strand | Q5SLM3 |
Ligands and binding sites
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 | 1135 | 0.83 | 0.84 | 106 | GOL |
| 2 | 634 | 0.72 | 0.79 | 59 | ZN |
| 3 | 701 | 0.71 | 0.78 | 68 | empty |
| 4 | 612 | 0.69 | 0.78 | 63 | empty |
| 5 | 374 | 0.69 | 0.82 | 42 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1646 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 436 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5WVU · Crystal structure of carboxypeptidase from Thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SLM3 · AlphaFold monomer V2.0 prediction for thermostable carboxypeptidase 1 (Q5SLM3) · a predicted model of the same protein · 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 Q5SLM3
- Elsewhere: RCSB PDB 5WVU · PDBe 5WVU · UniProt Q5SLM3
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