Research workbench
Crystal structure of the hypc-hypd-hype complex (form I)
Analyse Crystal structure of the hypc-hypd-hype complex (form I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VYS
- Type
- protein
- Length
- 754 residues
- Chains
- 3
- 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, Q5JII7
- Ligands
- SF4, MG
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrogenase EXPRESSION/FORMATION protein hypc | protein | 53 | 0% helix, 55% strand | Q5JII0 |
| B | Hydrogenase EXPRESSION/FORMATION protein hypd | protein | 368 | 47% helix, 18% strand | Q5JII1 |
| C | Hydrogenase EXPRESSION/FORMATION protein hype | protein | 333 | 34% helix, 26% strand | Q5JII7 |
Ligands and binding sites
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 | 1170 | 0.86 | 0.87 | 106 | empty |
| 2 | 701 | 0.73 | 0.79 | 64 | MG |
| 3 | 115 | 0.49 | 0.80 | 31 | empty |
| 4 | 131 | 0.46 | 0.77 | 20 | empty |
| 5 | 75 | 0.32 | 0.75 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 960 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 960 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 422 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3VYS · Crystal structure of the HypC-HypD-HypE complex (form I) · 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
- Every structure of UniProt Q5JII7
- Elsewhere: RCSB PDB 3VYS · PDBe 3VYS · UniProt Q5JII0 · UniProt Q5JII1 · UniProt Q5JII7
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