Research workbench
A hyrdrogen producing hybrid streptavidin-diiron catalyst
Analyse A hyrdrogen producing hybrid streptavidin-diiron catalyst in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VCQ
- Type
- protein
- Length
- 482 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BN7
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Streptavidin | protein | 121 | 5% helix, 56% strand | P22629 |
| B, D | Streptavidin | protein | 120 | 5% helix, 55% strand | P22629 |
Ligands and binding sites
- BN7 · 2-methylpropyl 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate · ligand · 4 copies · chains A, C, B, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.68 | 0.84 | 49 | BN7 |
| 2 | 259 | 0.67 | 0.83 | 51 | BN7 |
| 3 | 364 | 0.65 | 0.80 | 56 | empty |
| 4 | 175 | 0.52 | 0.79 | 32 | empty |
| 5 | 157 | 0.51 | 0.79 | 31 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1643 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1617 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 528 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 522 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 221 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5VCQ · A Hyrdrogen Producing Hybrid Streptavidin-Diiron Catalyst · 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 P22629
- Elsewhere: RCSB PDB 5VCQ · PDBe 5VCQ · UniProt P22629
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