MolNFT v1 · #86658 · protein
Structure of the complex between smci and human carboxypeptidase A4
4BD9: “Structure of the complex between smci and human carboxypeptidase A4”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.71). MolNFT v1 #86658 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4BD9
- Type
- protein
- Length
- 469 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase A4; Carboxypeptidase inhibitor smci
- EC
- 3.4.17.-
- UniProt
- Q9UI42, P84875
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase A4 (EC 3.4.17.-) | protein | 304 | 38% helix, 18% strand | Q9UI42 |
| B | Carboxypeptidase inhibitor smci | protein | 165 | 18% helix, 27% strand | P84875 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.71 | 0.93 | 28 | empty |
| 2 | 178 | 0.55 | 0.80 | 22 | empty |
| 3 | 120 | 0.54 | 0.82 | 20 | empty |
| 4 | 165 | 0.50 | 0.78 | 25 | empty |
| 5 | 90 | 0.42 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1121 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4BD9 · Structure of the complex between SmCI and human carboxypeptidase A4 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UI42 · AlphaFold monomer V2.0 prediction for carboxypeptidase A4 (Q9UI42) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P84875 · AlphaFold monomer V2.0 prediction for carboxypeptidase inhibitor smci (P84875) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9UI42
- Every structure of UniProt P84875
- Elsewhere: RCSB PDB 4BD9 · PDBe 4BD9 · UniProt Q9UI42 · UniProt P84875
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