Research workbench
Pro-carboxypeptidase U in complex with 5-(3-aminopropyl)-1-propyl-6,7- dihydro-4H-benzimidazole-5-carboxylic acid
Analyse Pro-carboxypeptidase U in complex with 5-(3-aminopropyl)-1-propyl-6,7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P10
- Type
- protein
- Length
- 402 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase B2
- EC
- 3.4.17.20
- UniProt
- Q96IY4
- Ligands
- 2B8, NAG, ZN
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase B2 (EC 3.4.17.20) | protein | 402 | 39% helix, 19% strand | Q96IY4 |
Ligands and binding sites
- 2B8 · (5R)-5-(3-aminopropyl)-1-propyl-4,5,6,7-tetrahydro-1H-benzimidazole-5-carboxylic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.78 | 0.91 | 34 | 2B8, DMS |
| 2 | 156 | 0.40 | 0.73 | 33 | empty |
| 3 | 57 | 0.39 | 0.80 | 17 | empty |
| 4 | 63 | 0.27 | 0.72 | 14 | empty |
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4P10 · pro-carboxypeptidase U In Complex With 5-(3-aminopropyl)-1-propyl-6,7-dihydro-4H-benzimida… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96IY4 · AlphaFold monomer V2.0 prediction for carboxypeptidase B2 (Q96IY4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q96IY4
- Elsewhere: RCSB PDB 4P10 · PDBe 4P10 · UniProt Q96IY4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.