Research workbench
Crystal structure of pepa from streptococcus pneumoniae
Analyse Crystal structure of pepa from streptococcus pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KL9
- Type
- protein
- Length
- 4,056 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamyl aminopeptidase
- EC
- 3.4.11.7
- UniProt
- Q8DNJ7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, K | Glutamyl aminopeptidase (EC 3.4.11.7) | protein | 340 | 31% helix, 29% strand | Q8DNJ7 |
| B, C, F, G, H, I, J, L | Glutamyl aminopeptidase (EC 3.4.11.7) | protein | 337 | 31% helix, 29% strand | Q8DNJ7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 191 | 0.56 | 0.80 | 34 | empty |
| 2 | 327 | 0.55 | 0.75 | 54 | ZN |
| 3 | 194 | 0.55 | 0.79 | 31 | empty |
| 4 | 291 | 0.54 | 0.76 | 47 | ZN |
| 5 | 348 | 0.54 | 0.74 | 53 | ZN |
Interfaces
18 interfaces between chains.
- A–D · 1685 Ų buried · 30 hydrogen bonds · protein-protein
- F–K · 1680 Ų buried · 31 hydrogen bonds · protein-protein
- B–G · 1674 Ų buried · 27 hydrogen bonds · protein-protein
- I–L · 1670 Ų buried · 28 hydrogen bonds · protein-protein
- C–J · 1664 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3KL9 · Crystal structure of PepA from Streptococcus pneumoniae · the same entry in another collection · chain K against K, 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 Q8DNJ7
- Elsewhere: RCSB PDB 3KL9 · PDBe 3KL9 · UniProt Q8DNJ7
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