Research workbench
Crystal structure of the hypc-hypd complex
Analyse Crystal structure of the hypc-hypd complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VYR
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase EXPRESSION/FORMATION protein hypc; Hydrogenase EXPRESSION/FORMATION protein…
- UniProt
- Q5JII0, Q5JII1
- Ligands
- SF4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrogenase EXPRESSION/FORMATION protein hypc | protein | 72 | 26% helix, 40% strand | Q5JII0 |
| B | Hydrogenase EXPRESSION/FORMATION protein hypd | protein | 371 | 45% helix, 18% strand | Q5JII1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.72 | 0.80 | 62 | CIT |
| 2 | 198 | 0.48 | 0.75 | 38 | empty |
| 3 | 172 | 0.46 | 0.75 | 20 | empty |
| 4 | 113 | 0.39 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1145 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3VYR · Crystal structure of the HypC-HypD complex · 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 Q5JII0
- Every structure of UniProt Q5JII1
- Elsewhere: RCSB PDB 3VYR · PDBe 3VYR · UniProt Q5JII0 · UniProt Q5JII1
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