MolNFT v1 · #28882 · protein
Structure of the ready oxidized form of [nife]-hydrogenase
1YRQ · Periplasmic [nife] hydrogenase small subunit: “Structure of the ready oxidized form of [nife]-hydrogenase”. X-ray diffraction, 5 ligands (SF4, F3S, FCO), 20 pockets (best druggability 0.82). MolNFT v1 #28882 on GenesisL1: 3D…
- PDB
- 1YRQ
- Type
- protein
- Length
- 4,836 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic [nife] hydrogenase small subunit; Periplasmic [nife] hydrogenase large subunit
- EC
- 1.12.2.1
- UniProt
- P18187, P18188
- Ligands
- SF4, F3S, FCO, NI, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, G | Periplasmic [nife] hydrogenase small subunit (EC 1.12.2.1) | protein | 262 | 38% helix, 17% strand | P18187 |
| H, I, M, N | Periplasmic [nife] hydrogenase large subunit (EC 1.12.2.1) | protein | 545 | 49% helix, 16% strand | P18188 |
| C, F | Periplasmic [nife] hydrogenase small subunit (EC 1.12.2.1) | protein | 260 | 37% helix, 17% strand | P18187 |
| J, K | Periplasmic [nife] hydrogenase large subunit (EC 1.12.2.1) | protein | 544 | 48% helix, 16% strand | P18188 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 12 copies · chains A, H, B, I, C, J, D, K, F, M, G, N
- F3S · FE3-S4 cluster · ligand · 6 copies · chains A, H, B, I, C, J, D, K, F, M, G, N
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 6 copies · chains H, I, J, K, M, N
- NI · Nickel (II) ion · metal · 6 copies · chains H, I, J, K, M, N
- MG · Magnesium ion · metal · 6 copies · chains H, I, J, K, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.82 | 0.96 | 59 | empty |
| 2 | 1093 | 0.81 | 0.82 | 138 | empty |
| 3 | 172 | 0.81 | 0.95 | 56 | empty |
| 4 | 1082 | 0.80 | 0.81 | 77 | empty |
| 5 | 1073 | 0.80 | 0.81 | 75 | empty |
Interfaces
22 interfaces between chains.
- G–N · 3606 Ų buried · 54 hydrogen bonds · protein-protein
- A–H · 3599 Ų buried · 56 hydrogen bonds · protein-protein
- D–K · 3591 Ų buried · 55 hydrogen bonds · protein-protein
- B–I · 3582 Ų buried · 57 hydrogen bonds · protein-protein
- F–M · 3566 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1YRQ · Structure of the ready oxidized form of [NiFe]-hydrogenase · the same entry in another collection · chain N against N, 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 P18187
- Every structure of UniProt P18188
- Elsewhere: RCSB PDB 1YRQ · PDBe 1YRQ · UniProt P18187 · UniProt P18188
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