MolNFT v1 · #161569 · protein
Xenon derivatization of the F420-reducing [nife] hydrogenase complex from methanosarcina barkeri
6QII · Coenzyme F420 hydrogenase subunit gamma: “Xenon derivatization of the F420-reducing [nife] hydrogenase complex from methanosarcina barkeri”. X-ray diffraction, 7 ligands (SF4, FES, NFU), 12 pockets (best druggability 0.82). MolNFT…
- PDB
- 6QII
- Type
- protein
- Length
- 981 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420 hydrogenase subunit gamma; Coenzyme F420 hydrogenase subunit alpha…
- EC
- 1.12.98.1
- UniProt
- A0A0E3LP72, A0A1D2X0K1
- Ligands
- SF4, FES, NFU, FAD, FE, MG, XE
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Coenzyme F420 hydrogenase subunit gamma (EC 1.12.98.1) | protein | 253 | 43% helix, 17% strand | A0A0E3LP72 |
| A | Coenzyme F420 hydrogenase subunit alpha | protein | 437 | 41% helix, 20% strand | — |
| B | Coenzyme F420 hydrogenase subunit beta | protein | 291 | 35% helix, 24% strand | A0A1D2X0K1 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains G, A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · chains G
- NFU · formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains B
- FE · Fe (III) ion · metal · chains G, A
- MG · Magnesium ion · metal · chains A
- XE · Xenon · ion · 7 copies · chains G, A
- BU3 · (R,R)-2,3-butanediol · additive · 7 copies · chains G, A, B
- 144 · Tris-hydroxymethyl-methyl-ammonium · additive · 2 copies · chains G, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.82 | 0.87 | 75 | FAD, SF4 |
| 2 | 431 | 0.79 | 0.87 | 68 | XE |
| 3 | 430 | 0.62 | 0.77 | 48 | BU3 |
| 4 | 238 | 0.59 | 0.80 | 44 | 144 |
| 5 | 273 | 0.59 | 0.78 | 40 | BU3 |
Interfaces
3 interfaces between chains.
- G–A · 2599 Ų buried · 44 hydrogen bonds · protein-protein
- G–B · 2202 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 588 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6QII · Xenon derivatization of the F420-reducing [NiFe] hydrogenase complex from Methanosarcina… · the same entry in another collection · chain G against G, 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 A0A0E3LP72
- Every structure of UniProt A0A1D2X0K1
- Elsewhere: RCSB PDB 6QII · PDBe 6QII · UniProt A0A0E3LP72 · UniProt A0A1D2X0K1
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