Research workbench
2.6 ångström resolution crystal structure of aminopeptidase B from escherichia COLI str. K-12 substr. MG1655
Analyse 2.6 ångström resolution crystal structure of aminopeptidase B from escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OV8
- Type
- protein
- Length
- 2,564 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase B
- EC
- 3.4.11.23
- UniProt
- P37095
- Ligands
- ZN, MN, CL
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Peptidase B (EC 3.4.11.23) | protein | 429 | 37% helix, 21% strand | P37095 |
| B, C | Peptidase B (EC 3.4.11.23) | protein | 426 | 36% helix, 21% strand | P37095 |
| D, F | Peptidase B (EC 3.4.11.23) | protein | 427 | 38% helix, 21% strand | P37095 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 21 copies · chains A, E, B, F, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.65 | 0.77 | 63 | empty |
| 2 | 322 | 0.64 | 0.80 | 37 | empty |
| 3 | 435 | 0.64 | 0.78 | 51 | empty |
| 4 | 326 | 0.63 | 0.79 | 34 | empty |
| 5 | 359 | 0.63 | 0.78 | 50 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1044 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1033 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 1030 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1029 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1013 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered).
Compared structures
- 6OV8 · 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str.… · the same entry in another collection · chain E against E, TM-score 1.00
- P37095 · AlphaFold monomer V2.0 prediction for peptidase B (P37095) · a predicted model of the same protein · chain D 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 P37095
- Elsewhere: RCSB PDB 6OV8 · PDBe 6OV8 · UniProt P37095
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.