MolNFT v1 · #60379 · protein
Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from cytophaga hutchinsonii atcc 33406 at 2.39 a resolution
3CPX · Aminopeptidase, M42 family: “Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from cytophaga hutchinsonii atcc…”. X-ray diffraction, 2 ligands (FE, CL), 4 pockets (best druggability 0.78). MolNFT v1 #60379 on…
- PDB
- 3CPX
- Type
- protein
- Length
- 929 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase, M42 family
- UniProt
- Q11Z05
- Ligands
- FE, CL
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aminopeptidase, M42 family | protein | 309 | 31% helix, 28% strand | Q11Z05 |
| B | Aminopeptidase, M42 family | protein | 311 | 32% helix, 28% strand | Q11Z05 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 6 copies · chains A, B, C
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.78 | 0.81 | 106 | FE, EDO, CL |
| 2 | 93 | 0.35 | 0.74 | 23 | empty |
| 3 | 93 | 0.35 | 0.75 | 18 | empty |
| 4 | 68 | 0.29 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1204 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1201 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1189 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 3CPX · Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga… · the same entry in another collection · 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 Q11Z05
- Elsewhere: RCSB PDB 3CPX · PDBe 3CPX · UniProt Q11Z05
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