MolNFT v1 · #82820 · protein
Crystal structure of the hypc-hypd-hype complex (form I inward)
3VYT · Hydrogenase EXPRESSION/FORMATION protein hypc: “Crystal structure of the hypc-hypd-hype complex (form I inward)”. X-ray diffraction, 3 ligands (SF4, MG, CL), 5 pockets (best druggability 0.86). MolNFT v1 #82820 on GenesisL1: 3D…
- PDB
- 3VYT
- Type
- protein
- Length
- 756 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, CL
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrogenase EXPRESSION/FORMATION protein hypc | protein | 52 | 0% helix, 58% strand | Q5JII0 |
| B | Hydrogenase EXPRESSION/FORMATION protein hypd | protein | 368 | 44% helix, 18% strand | Q5JII1 |
| C | Hydrogenase EXPRESSION/FORMATION protein hype | protein | 336 | 33% helix, 25% strand | Q5JII7 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains B
- MG · Magnesium ion · metal · 5 copies · chains C
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.86 | 0.87 | 105 | empty |
| 2 | 395 | 0.69 | 0.82 | 51 | MG, CL |
| 3 | 138 | 0.51 | 0.80 | 31 | empty |
| 4 | 138 | 0.45 | 0.76 | 19 | empty |
| 5 | 77 | 0.34 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 897 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 891 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3VYT · Crystal structure of the HypC-HypD-HypE complex (form I inward) · 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 3VYT · PDBe 3VYT · UniProt Q5JII0 · UniProt Q5JII1 · UniProt Q5JII7
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