MolNFT v1 · #38057 · protein
Crystal structure of aminipeptidase (M18 family) from thermotoga maritima
2GLF · Probable M18-family aminopeptidase 1: “Crystal structure of aminipeptidase (M18 family) from thermotoga maritima”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.84). MolNFT v1 #38057 on GenesisL1: 3D structure…
- PDB
- 2GLF
- Type
- protein
- Length
- 1,800 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable M18-family aminopeptidase 1
- EC
- 3.4.11.-
- UniProt
- Q9WYJ9
- Ligands
- MN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Probable M18-family aminopeptidase 1 (EC 3.4.11.-) | protein | 450 | 33% helix, 24% strand | Q9WYJ9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.84 | 0.86 | 91 | MN |
| 2 | 260 | 0.60 | 0.80 | 52 | MN |
| 3 | 321 | 0.59 | 0.77 | 49 | empty |
| 4 | 332 | 0.59 | 0.77 | 43 | empty |
| 5 | 238 | 0.56 | 0.78 | 43 | MN |
Interfaces
4 interfaces between chains.
- A–D · 4238 Ų buried · 59 hydrogen bonds · protein-protein
- B–D · 2241 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 2224 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 2201 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered).
Compared structures
- 2GLF · Crystal structure of Aminipeptidase (M18 family) from Thermotoga Maritima · the same entry in another collection · chain D against D, TM-score 1.00
- Q9WYJ9 · AlphaFold monomer V2.0 prediction for probable M18 family aminopeptidase 1 (Q9WYJ9) · a predicted model of the same protein · chain C 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 Q9WYJ9
- Elsewhere: RCSB PDB 2GLF · PDBe 2GLF · UniProt Q9WYJ9
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