MolNFT v1 · #113792 · protein
The structure of the transthyretin-like domain of the first catalytic domain of the human carboxypeptidase D
5AQ0: “The structure of the transthyretin-like domain of the first catalytic domain of the human carboxypeptidase D”. X-ray diffraction, 2 pockets (best druggability 0.53). MolNFT v1 #113792 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5AQ0
- Type
- protein
- Length
- 163 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase D
- EC
- 3.4.17.22
- UniProt
- O75976
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase D (EC 3.4.17.22) | protein | 81 | 0% helix, 53% strand | O75976 |
| B | Carboxypeptidase D (EC 3.4.17.22) | protein | 82 | 0% helix, 57% strand | O75976 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.53 | 0.78 | 32 | GOL |
| 2 | 87 | 0.40 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 370 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5AQ0 · The structure of the Transthyretin-like domain of the first catalytic domain of the HUMAN… · the same entry in another collection · chain A against A, TM-score 1.00
- O75976 · AlphaFold monomer V2.0 prediction for carboxypeptidase D (O75976) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 O75976
- Elsewhere: RCSB PDB 5AQ0 · PDBe 5AQ0 · UniProt O75976
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