Research workbench
Crystal structure of hypa in the dimeric form
Analyse Crystal structure of hypa in the dimeric form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A44
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase nickel incorporation protein hypa
- UniProt
- Q5JIH3
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrogenase nickel incorporation protein hypa | protein | 137 | 36% helix, 28% strand | Q5JIH3 |
| B | Hydrogenase nickel incorporation protein hypa | protein | 132 | 30% helix, 29% strand | Q5JIH3 |
| C | Hydrogenase nickel incorporation protein hypa | protein | 122 | 28% helix, 30% strand | Q5JIH3 |
| D | Hydrogenase nickel incorporation protein hypa | protein | 127 | 31% helix, 28% strand | Q5JIH3 |
Ligands and binding sites
- ZN · Zinc 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.57 | 0.76 | 42 | empty |
| 2 | 264 | 0.53 | 0.75 | 24 | empty |
| 3 | 166 | 0.42 | 0.74 | 30 | empty |
| 4 | 52 | 0.37 | 0.80 | 12 | empty |
| 5 | 73 | 0.32 | 0.75 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3318 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2750 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 252 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 184 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 177 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (formylation).
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 Q5JIH3
- Elsewhere: RCSB PDB 3A44 · PDBe 3A44 · UniProt Q5JIH3
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