Research workbench
Crystal structure of putative xaa-his dipeptidase (YP_718209.1) from haemophilus somnus 129PT at 2.11 a resolution
Analyse Crystal structure of putative xaa-his dipeptidase (YP_718209.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QYV
- Type
- protein
- Length
- 942 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaa-his dipeptidase
- EC
- 3.4.13.20
- UniProt
- Q0I1B9
- Ligands
- ZN, SO4
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xaa-his dipeptidase (EC 3.4.13.20) | protein | 472 | 31% helix, 30% strand | Q0I1B9 |
| B | Xaa-his dipeptidase (EC 3.4.13.20) | protein | 470 | 31% helix, 30% strand | Q0I1B9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 18 copies · chains A, B
- GOL · Glycerol · additive · 17 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.86 | 0.89 | 71 | GOL |
| 2 | 537 | 0.73 | 0.82 | 63 | ZN, SO4 |
| 3 | 335 | 0.71 | 0.84 | 46 | ZN, SO4 |
| 4 | 99 | 0.39 | 0.76 | 21 | GOL |
| 5 | 69 | 0.38 | 0.78 | 17 | GOL |
Interfaces
1 interface between chains.
- A–B · 1291 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2QYV · Crystal structure of putative Xaa-His dipeptidase (YP_718209.1) from Haemophilus somnus… · 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 Q0I1B9
- Elsewhere: RCSB PDB 2QYV · PDBe 2QYV · UniProt Q0I1B9
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