MolNFT v1 · #139423 · protein
Crystal structure of NAD+-reducing [nife]-hydrogenase in the air- oxidized state
5XF9 · NAD-reducing hydrogenase: “Crystal structure of NAD+-reducing [nife]-hydrogenase in the air- oxidized state”. X-ray diffraction, 6 ligands (SF4, FMN, FES), 20 pockets (best druggability 0.82). MolNFT v1 #139423 on GenesisL1: 3D…
- PDB
- 5XF9
- Type
- protein
- Length
- 2,875 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-reducing hydrogenase
- UniProt
- A0A077L6X8, A0A077L885, A0A077L7R5, A0A077LAI5
- Ligands
- SF4, FMN, FES, FCO, 3NI, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-reducing hydrogenase | protein | 576 | 46% helix, 15% strand | A0A077L6X8 |
| B | NAD-reducing hydrogenase | protein | 234 | 27% helix, 18% strand | A0A077L885 |
| C, G | NAD-reducing hydrogenase | protein | 178 | 38% helix, 22% strand | A0A077L7R5 |
| D | NAD-reducing hydrogenase | protein | 455 | 49% helix, 18% strand | A0A077LAI5 |
| E | NAD-reducing hydrogenase | protein | 567 | 47% helix, 15% strand | A0A077L6X8 |
| F | NAD-reducing hydrogenase | protein | 233 | 27% helix, 18% strand | A0A077L885 |
| H | NAD-reducing hydrogenase | protein | 454 | 50% helix, 18% strand | A0A077LAI5 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, E
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, F
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains D, H
- 3NI · Nickel (III) ion · metal · 2 copies · chains D, H
- MG · Magnesium ion · metal · 2 copies · chains D, H
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 | 699 | 0.82 | 0.86 | 79 | FMN |
| 2 | 437 | 0.82 | 0.90 | 77 | empty |
| 3 | 596 | 0.81 | 0.87 | 62 | FMN |
| 4 | 121 | 0.80 | 0.98 | 32 | empty |
| 5 | 125 | 0.80 | 0.98 | 32 | empty |
Interfaces
16 interfaces between chains.
- G–H · 2848 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2819 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2067 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2059 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1149 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5XF9 · Crystal structure of NAD+-reducing [NiFe]-hydrogenase in the air-oxidized state · 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 A0A077L6X8
- Every structure of UniProt A0A077L885
- Every structure of UniProt A0A077L7R5
- Every structure of UniProt A0A077LAI5
- Elsewhere: RCSB PDB 5XF9 · PDBe 5XF9 · UniProt A0A077L6X8 · UniProt A0A077L885 · UniProt A0A077L7R5 · UniProt A0A077LAI5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.