Research workbench
Crystal structure of deblocking aminopeptidase from bacillus cereus
Analyse Crystal structure of deblocking aminopeptidase from bacillus cereus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GRE
- Type
- protein
- Length
- 4,918 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deblocking aminopeptidase
- EC
- 3.4.11.-
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 15 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 313 | 25% helix, 33% strand | — |
| B | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 312 | 25% helix, 33% strand | — |
| C | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 308 | 25% helix, 33% strand | — |
| D | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 306 | 26% helix, 32% strand | — |
| E | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 306 | 25% helix, 33% strand | — |
| F, L | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 310 | 25% helix, 32% strand | — |
| G | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 309 | 24% helix, 35% strand | — |
| H | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 305 | 27% helix, 33% strand | — |
| I | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 299 | 25% helix, 34% strand | — |
| J | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 307 | 25% helix, 33% strand | — |
| K | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 304 | 26% helix, 33% strand | — |
| M | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 309 | 26% helix, 33% strand | — |
| N | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 307 | 25% helix, 34% strand | — |
| O | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 308 | 26% helix, 33% strand | — |
| P | Deblocking aminopeptidase (EC 3.4.11.-) | protein | 305 | 26% helix, 33% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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 | 971 | 0.81 | 0.82 | 129 | empty |
| 2 | 639 | 0.77 | 0.83 | 89 | empty |
| 3 | 643 | 0.76 | 0.82 | 78 | empty |
| 4 | 760 | 0.76 | 0.80 | 97 | empty |
| 5 | 456 | 0.74 | 0.83 | 67 | empty |
Interfaces
22 interfaces between chains.
- C–E · 1483 Ų buried · 31 hydrogen bonds · protein-protein
- F–L · 1459 Ų buried · 30 hydrogen bonds · protein-protein
- D–H · 1454 Ų buried · 26 hydrogen bonds · protein-protein
- I–K · 1449 Ų buried · 27 hydrogen bonds · protein-protein
- O–P · 1429 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 96 modified (engineered).
Compared structures
- 2GRE · Crystal structure of Deblocking aminopeptidase from Bacillus cereus · 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
- Elsewhere: RCSB PDB 2GRE · PDBe 2GRE
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