MolNFT v1 · #119898 · protein
Crystal structure of M32 carboxypeptidase from deinococcus radiodurans R1
5GIV · Carboxypeptidase 1: “Crystal structure of M32 carboxypeptidase from deinococcus radiodurans R1”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.71). MolNFT v1 #119898 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5GIV
- Type
- protein
- Length
- 2,988 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase 1
- EC
- 3.4.17.19
- UniProt
- Q9RRR3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Carboxypeptidase 1 (EC 3.4.17.19) | protein | 497 | 67% helix, 3% strand | Q9RRR3 |
| B, F | Carboxypeptidase 1 (EC 3.4.17.19) | protein | 501 | 67% helix, 3% strand | Q9RRR3 |
| C | Carboxypeptidase 1 (EC 3.4.17.19) | protein | 495 | 68% helix, 3% strand | Q9RRR3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.71 | 0.82 | 50 | ACT |
| 2 | 493 | 0.71 | 0.81 | 50 | ZN |
| 3 | 701 | 0.70 | 0.77 | 73 | empty |
| 4 | 378 | 0.70 | 0.83 | 48 | ZN |
| 5 | 371 | 0.70 | 0.83 | 47 | empty |
Interfaces
5 interfaces between chains.
- B–F · 1446 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 1430 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1430 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 243 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 102 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5GIV · Crystal structure of M32 carboxypeptidase from Deinococcus radiodurans R1 · 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 Q9RRR3
- Elsewhere: RCSB PDB 5GIV · PDBe 5GIV · UniProt Q9RRR3
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