Research workbench
Crystal structure of porcine aminopeptidase-N with methionine
Analyse Crystal structure of porcine aminopeptidase-N with methionine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BV4
- Type
- protein
- Length
- 902 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- P15145
- Ligands
- MET, NAG, ZN, SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 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 |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 12 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.71 | 0.75 | 84 | MET, SO4 |
| 2 | 472 | 0.63 | 0.76 | 47 | empty |
| 3 | 330 | 0.61 | 0.78 | 38 | empty |
| 4 | 77 | 0.37 | 0.77 | 15 | SO4 |
| 5 | 100 | 0.36 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 11 glycan, 2 disulfide (N-glycosylation, 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 P15145
- Elsewhere: RCSB PDB 6BV4 · PDBe 6BV4 · UniProt P15145
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