MolNFT v1 · #102232 · protein
Crystal structure of ynta from yersinia pestis, unliganded form
4OFO · Extracytoplasmic nickel-binding protein ypynta: “Crystal structure of ynta from yersinia pestis, unliganded form”. X-ray diffraction, 1 ligand (NI), 16 pockets (best druggability 0.85). MolNFT v1 #102232 on GenesisL1: 3D structure…
- PDB
- 4OFO
- Type
- protein
- Length
- 1,988 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracytoplasmic nickel-binding protein ypynta
- UniProt
- Q7CJS8
- Ligands
- NI
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Extracytoplasmic nickel-binding protein ypynta | protein | 497 | 26% helix, 25% strand | Q7CJS8 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.85 | 0.86 | 146 | empty |
| 2 | 712 | 0.81 | 0.85 | 87 | empty |
| 3 | 1179 | 0.78 | 0.80 | 102 | empty |
| 4 | 327 | 0.77 | 0.88 | 48 | empty |
| 5 | 234 | 0.59 | 0.79 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–B · 911 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 904 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 581 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4OFO · Crystal structure of YntA from Yersinia pestis, unliganded form · 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 4OFO · PDBe 4OFO · UniProt Q7CJS8
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