MolNFT v1 · #141154 · protein
Crystal structure of the hyhl-hypa complex (form II)
5YY0 · Cytosolic nife-hydrogenase, alpha subunit: “Crystal structure of the hyhl-hypa complex (form II)”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.79). MolNFT v1 #141154 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YY0
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosolic nife-hydrogenase, alpha subunit; Probable hydrogenase nickel incorporation…
- UniProt
- Q8NKS2, Q5JIH3
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic nife-hydrogenase, alpha subunit | protein | 400 | 45% helix, 16% strand | Q8NKS2 |
| B | Probable hydrogenase nickel incorporation protein hypa | protein | 126 | 30% helix, 31% strand | Q5JIH3 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.79 | 0.83 | 106 | empty |
| 2 | 163 | 0.72 | 0.90 | 25 | empty |
| 3 | 106 | 0.58 | 0.85 | 27 | empty |
| 4 | 159 | 0.53 | 0.79 | 21 | empty |
| 5 | 75 | 0.33 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 739 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 Q8NKS2
- Every structure of UniProt Q5JIH3
- Elsewhere: RCSB PDB 5YY0 · PDBe 5YY0 · UniProt Q8NKS2 · UniProt Q5JIH3
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