MolNFT v1 · #102229 · protein
Crystal structure of ynta from yersinia pestis in complex with NI(L- HIS)2
4OFL · Extracytoplasmic nickel-binding protein ypynta: “Crystal structure of ynta from yersinia pestis in complex with NI(L- HIS)2”. X-ray diffraction, 2 ligands (HIS, NI), 8 pockets (best druggability 0.83). MolNFT v1 #102229 on…
- PDB
- 4OFL
- Type
- protein
- Length
- 992 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracytoplasmic nickel-binding protein ypynta
- UniProt
- Q7CJS8
- Ligands
- HIS, NI
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Extracytoplasmic nickel-binding protein ypynta | protein | 496 | 26% helix, 25% strand | Q7CJS8 |
Ligands and binding sites
- HIS · Histidine · ligand · 4 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.83 | 0.84 | 100 | HIS |
| 2 | 917 | 0.81 | 0.83 | 78 | NI, HIS |
| 3 | 570 | 0.80 | 0.86 | 73 | empty |
| 4 | 198 | 0.54 | 0.78 | 26 | empty |
| 5 | 83 | 0.46 | 0.81 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1274 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4OFL · Crystal structure of YntA from Yersinia pestis in complex with Ni(L-His)2 · 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 Q7CJS8
- Elsewhere: RCSB PDB 4OFL · PDBe 4OFL · UniProt Q7CJS8
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