MolNFT v1 · #126294 · protein
Crystal structure of 1 in complex with tafcpb
5LYF · Carboxypeptidase B: “Crystal structure of 1 in complex with tafcpb”. X-ray diffraction, 2 ligands (7B6, ZN), 1 pocket (best druggability 0.57). MolNFT v1 #126294 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LYF
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase B
- EC
- 3.4.17.2
- UniProt
- P09955
- Ligands
- 7B6, ZN
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase B (EC 3.4.17.2) | protein | 305 | 37% helix, 16% strand | P09955 |
Ligands and binding sites
- 7B6 · (2~{S})-6-azanyl-2-[[(2~{R})-1-[[(1~{R},2~{S},4~{S})-2-bicyclo[2.2.1]heptanyl]amino]-3-cyclohexyl-1-oxidanylidene-propan-2-yl]carbamoylamino]hexanoic acid · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.57 | 0.88 | 21 | 7B6 |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 P09955
- Elsewhere: RCSB PDB 5LYF · PDBe 5LYF · UniProt P09955
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