MolNFT v1 · #129201 · protein
Heterodisulfide reductase / [nife]-hydrogenase complex from methanothermococcus thermolithotrophicus at 2.3 a resolution
5ODC: “Heterodisulfide reductase / [nife]-hydrogenase complex from methanothermococcus thermolithotrophicus at 2.3 a…”. X-ray diffraction, 8 ligands (SF4, 9S8, FAD). MolNFT v1 #129201 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5ODC
- Type
- protein
- Length
- 4,011 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Ligands
- SF4, 9S8, FAD, FES, NFU, NA, CA, MG
Structure
x-ray diffraction · 7 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | — | protein | 653 | — | — |
| B, H | — | protein | 291 | — | — |
| C | — | protein | 184 | — | — |
| D, J | — | protein | 138 | — | — |
| E, K | — | protein | 298 | — | — |
| F, L | — | protein | 447 | — | — |
| I | — | protein | 173 | — | — |
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
- 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
- NA · Sodium ion · metal · 2 copies · chains A, G
- CA · Calcium ion · metal · 2 copies · chains F, L
- MG · Magnesium ion · metal · 2 copies · chains E, F, I
- GOL · Glycerol · additive · 15 copies · chains A, C, D, B, E, G, I, J, K, L
- ACT · Acetate ion · additive · 5 copies · chains A, G, B, F, C
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · chains A, 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.
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5ODC · PDBe 5ODC
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