MolNFT v1 · #113856 · protein
Crystal structure of the hypab complex
5AUP · Probable hydrogenase nickel incorporation protein hypa: “Crystal structure of the hypab complex”. X-ray diffraction, 3 ligands (ACP, ZN, MG), 6 pockets (best druggability 0.89). MolNFT v1 #113856 on GenesisL1: 3D structure, binding…
- PDB
- 5AUP
- Type
- protein
- Length
- 752 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable hydrogenase nickel incorporation protein hypa; ATPase involved in chromosome…
- UniProt
- Q5JIH3, Q5JIH4
- Ligands
- ACP, ZN, MG
- Pockets
- 6 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable hydrogenase nickel incorporation protein hypa | protein | 136 | 37% helix, 28% strand | Q5JIH3 |
| B | ATPase involved in chromosome partitioning, PARA/MIND family, mrp homolog | protein | 240 | 38% helix, 22% strand | Q5JIH4 |
| H | Probable hydrogenase nickel incorporation protein hypa | protein | 135 | 35% helix, 28% strand | Q5JIH3 |
| I | ATPase involved in chromosome partitioning, PARA/MIND family, mrp homolog | protein | 241 | 39% helix, 21% strand | Q5JIH4 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains B, I
- ZN · Zinc ion · metal · 2 copies · chains A, H
- MG · Magnesium ion · metal · 2 copies · chains B, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.89 | 0.91 | 86 | ACP, MG |
| 2 | 615 | 0.65 | 0.76 | 60 | empty |
| 3 | 89 | 0.48 | 0.82 | 22 | empty |
| 4 | 59 | 0.36 | 0.78 | 12 | empty |
| 5 | 62 | 0.28 | 0.73 | 14 | empty |
Interfaces
5 interfaces between chains.
- B–I · 1900 Ų buried · 28 hydrogen bonds · protein-protein
- B–H · 1633 Ų buried · 21 hydrogen bonds · protein-protein
- A–I · 1588 Ų buried · 22 hydrogen bonds · protein-protein
- H–I · 280 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 275 Ų buried · 4 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 Q5JIH3
- Every structure of UniProt Q5JIH4
- Elsewhere: RCSB PDB 5AUP · PDBe 5AUP · UniProt Q5JIH3 · UniProt Q5JIH4
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