MolNFT v1 · #110111 · protein
Crystal structure of MET260ALA mutant of E. COLI aminopeptidase N in complex with L-2,3-diaminopropionic acid
4XMT: “Crystal structure of MET260ALA mutant of E. COLI aminopeptidase N in complex with L-2,3-diaminopropionic acid”. X-ray diffraction, 3 ligands (DPP, NA, ZN), 10 pockets (best druggability 0.84). MolNFT v1 #110111 on GenesisL1: 3D…
- PDB
- 4XMT
- Type
- protein
- Length
- 867 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- P04825
- Ligands
- DPP, NA, ZN
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 867 | 44% helix, 22% strand | P04825 |
Ligands and binding sites
- DPP · Diaminopropanoic acid · ligand · chains A
- NA · Sodium ion · metal · 7 copies · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 9 copies · chains A
- MLI · Malonate ion · additive · chains A
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 | 1180 | 0.84 | 0.85 | 122 | ZN, DPP, GOL, MLI |
| 2 | 494 | 0.73 | 0.81 | 59 | GOL |
| 3 | 686 | 0.70 | 0.78 | 57 | empty |
| 4 | 76 | 0.59 | 0.88 | 21 | empty |
| 5 | 145 | 0.47 | 0.78 | 33 | empty |
Compared structures
- 4XMT · Crystal Structure of Met260Ala mutant of E. coli Aminopeptidase N in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P04825 · AlphaFold monomer V2.0 prediction for aminopeptidase N (P04825) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P04825
- Elsewhere: RCSB PDB 4XMT · PDBe 4XMT · UniProt P04825
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