MolNFT v1 · #38061 · protein
Crystal structure of aminopeptidase I from clostridium acetobutylicum
2GLJ · Probable M18-family aminopeptidase 1: “Crystal structure of aminopeptidase I from clostridium acetobutylicum”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.88). MolNFT v1 #38061 on GenesisL1: 3D structure…
- PDB
- 2GLJ
- Type
- protein
- Length
- 10,944 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable M18-family aminopeptidase 1
- EC
- 3.4.11.-
- UniProt
- Q97K30
- Ligands
- MN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | Probable M18-family aminopeptidase 1 (EC 3.4.11.-) | protein | 456 | 24% helix, 17% strand | Q97K30 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 48 copies · chains A, B, K, C, F, D, E, H, G, I, L, J, M, P, N, W, O, R, Q, T, S, V, U, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.88 | 0.90 | 119 | empty |
| 2 | 1021 | 0.88 | 0.89 | 118 | empty |
| 3 | 1040 | 0.88 | 0.89 | 115 | empty |
| 4 | 1054 | 0.87 | 0.88 | 124 | empty |
| 5 | 1171 | 0.87 | 0.88 | 147 | empty |
Interfaces
46 interfaces between chains.
- A–D · 4513 Ų buried · 54 hydrogen bonds · protein-protein
- C–F · 4512 Ų buried · 57 hydrogen bonds · protein-protein
- O–R · 4509 Ų buried · 58 hydrogen bonds · protein-protein
- B–K · 4503 Ų buried · 55 hydrogen bonds · protein-protein
- N–W · 4502 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 2GLJ · crystal structure of aminopeptidase I from Clostridium acetobutylicum · the same entry in another collection · chain I against I, 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 Q97K30
- Elsewhere: RCSB PDB 2GLJ · PDBe 2GLJ · UniProt Q97K30
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