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Crystal structure of porcine aminopeptidase N complexed with cngrcg tumor-homing peptide
Analyse Crystal structure of porcine aminopeptidase N complexed with cngrcg… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OU3
- Type
- protein
- Length
- 908 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N; Tumor-homing peptide
- EC
- 3.4.11.2
- UniProt
- P15145
- Ligands
- NAG, ZN, SO4
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 902 | 44% helix, 20% strand | P15145 |
| B | Tumor-homing peptide | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A
- ZN · Zinc ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.64 | 0.76 | 47 | empty |
| 2 | 422 | 0.63 | 0.78 | 36 | empty |
| 3 | 219 | 0.60 | 0.81 | 31 | SO4 |
| 4 | 222 | 0.54 | 0.78 | 28 | empty |
| 5 | 102 | 0.37 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 428 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 4OU3 · Crystal structure of porcine aminopeptidase N complexed with CNGRCG tumor-homing peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P15145 · AlphaFold monomer V2.0 prediction for aminopeptidase N (P15145) · a predicted model of the same protein · chain A 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 P15145
- Elsewhere: RCSB PDB 4OU3 · PDBe 4OU3 · UniProt P15145
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