Research workbench
The F420-reducing [nife] hydrogenase complex from methanosarcina barkeri at the nia-S state
Analyse The F420-reducing [nife] hydrogenase complex from methanosarcina barkeri at the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QGR
- 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, A0A0E3QWH3
- Ligands
- SF4, FES, NFU, FAD, FE, MG
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Coenzyme F420 hydrogenase subunit gamma (EC 1.12.98.1) | protein | 253 | 45% helix, 17% strand | A0A0E3LP72 |
| A | Coenzyme F420 hydrogenase subunit alpha | protein | 437 | 42% helix, 20% strand | — |
| B | Coenzyme F420 hydrogenase subunit beta (EC 1.12.98.1) | protein | 291 | 36% helix, 25% strand | A0A0E3QWH3 |
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
- BU3 · (R,R)-2,3-butanediol · additive · 9 copies · chains G, B, A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains G, A
- 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.81 | 0.86 | 74 | FAD, SF4, BU3 |
| 2 | 400 | 0.78 | 0.86 | 57 | MPD |
| 3 | 424 | 0.62 | 0.77 | 47 | BU3 |
| 4 | 272 | 0.58 | 0.78 | 40 | BU3 |
| 5 | 173 | 0.54 | 0.80 | 31 | empty |
Interfaces
3 interfaces between chains.
- G–A · 2615 Ų buried · 50 hydrogen bonds · protein-protein
- G–B · 2174 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 586 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6QGR · The F420-reducing [NiFe] hydrogenase complex from Methanosarcina barkeri at the Nia-S… · 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 A0A0E3QWH3
- Elsewhere: RCSB PDB 6QGR · PDBe 6QGR · UniProt A0A0E3LP72 · UniProt A0A0E3QWH3
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