Research workbench
Heterodisulfide reductase / [nife]-hydrogenase complex from methanothermococcus thermolithotrophicus soaked with heterodisulfide for 3.5 minutes
Analyse Heterodisulfide reductase / [nife]-hydrogenase complex from methanothermococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ODH
- Type
- protein
- Length
- 4,019 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heterodisulfide reductase, subunit a; Heterodisulfide reductase, subunit B…
- EC
- 1.8.98.1, 1.12.1.2
- Ligands
- SF4, 9S8, FAD, COM, FES, NFU, TP7, FE
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 9 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heterodisulfide reductase, subunit a | protein | 652 | 29% helix, 25% strand | — |
| B, H | Heterodisulfide reductase, subunit B (EC 1.8.98.1) | protein | 291 | 55% helix, 11% strand | — |
| C | Heterodisulfide reductase, subunit C | protein | 184 | 58% helix, 4% strand | — |
| D | Methyl-viologen reducing hydrogenase, subunit D | protein | 137 | 49% helix, 17% strand | — |
| E, K | Methyl-viologen reducing hydrogenase, subunit G (EC 1.12.1.2) | protein | 298 | 35% helix, 15% strand | — |
| F, L | Methyl-viologen reducing hydrogenase, subunit a (EC 1.12.1.2) | protein | 447 | 50% helix, 19% strand | — |
| G | Heterodisulfide reductase, subunit a | protein | 653 | 31% helix, 26% strand | — |
| I | Heterodisulfide reductase, subunit C | protein | 183 | 58% helix, 4% strand | — |
| J | Methyl-viologen reducing hydrogenase, subunit D | protein | 138 | 49% helix, 18% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 22 copies · chains A, G, E, C, F, K, I, L
- 9S8 · Non-cubane [4Fe-4S]-cluster · ligand · 4 copies · chains B, C, H, I
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, G
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains B, C, H, I
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains D, J
- NFU · formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) · ligand · 2 copies · chains F, L
- TP7 · Coenzyme B · ligand · chains H, I
- FE · Fe (III) ion · metal · 3 copies · chains F, A, G, L
- GOL · Glycerol · additive · 6 copies · chains A, H, I, B, C, E, G, K
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 4 copies · chains A, G, F, L
- ACT · Acetate ion · additive · 2 copies · chains G
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D
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 | 646 | 0.88 | 0.93 | 71 | empty |
| 2 | 1074 | 0.82 | 0.83 | 87 | empty |
| 3 | 731 | 0.82 | 0.86 | 86 | FAD |
| 4 | 715 | 0.82 | 0.85 | 84 | FAD |
| 5 | 356 | 0.81 | 0.90 | 70 | SF4 |
Interfaces
24 interfaces between chains.
- E–F · 3695 Ų buried · 47 hydrogen bonds · protein-protein
- K–L · 3676 Ų buried · 55 hydrogen bonds · protein-protein
- A–G · 3441 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 3048 Ų buried · 50 hydrogen bonds · protein-protein
- H–I · 2956 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5ODH · Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus… · the same entry in another collection · chain K against K, 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
- Elsewhere: RCSB PDB 5ODH · PDBe 5ODH
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