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2.05 ångström resolution crystal structure of aminopeptidase B from escherichia COLI str. K-12 substr. MG1655.
Analyse 2.05 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
- 6OAD
- Type
- protein
- Length
- 5,109 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase B
- EC
- 3.4.11.23
- UniProt
- A0A387CSU7
- Ligands
- BCT, ZN, CA, CL
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, H, J, K | Peptidase B (EC 3.4.11.23) | protein | 426 | 37% helix, 21% strand | A0A387CSU7 |
| D, I, L | Peptidase B (EC 3.4.11.23) | protein | 425 | 36% helix, 20% strand | A0A387CSU7 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 19 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CA · Calcium ion · metal · 13 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 9 copies · chains A, B, C, E, F, K, L
- EDO · 1,2-ethanediol · additive · 39 copies · chains A, B, C, D, E, F, G, I, H, J, K, L
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains C, D, E, L
- PGE · Triethylene glycol · additive · chains A
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 | 805 | 0.71 | 0.77 | 69 | empty |
| 2 | 701 | 0.67 | 0.76 | 94 | EDO |
| 3 | 439 | 0.66 | 0.79 | 52 | BCT |
| 4 | 503 | 0.66 | 0.78 | 63 | BCT, EDO |
| 5 | 533 | 0.66 | 0.77 | 58 | empty |
Interfaces
26 interfaces between chains.
- G–L · 1030 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1029 Ų buried · 8 hydrogen bonds · protein-protein
- I–J · 1022 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 1019 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 1014 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6OAD · 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str.… · 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 A0A387CSU7
- Elsewhere: RCSB PDB 6OAD · PDBe 6OAD · UniProt A0A387CSU7
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