Research workbench
Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from methanospirillum hungatei (dimeric, composite structure)
Analyse Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BKC
- Type
- protein
- Length
- 8,220 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cob--com heterodisulfide reductase iron-sulfur subunit a; F420-non-reducing hydrogenase…
- EC
- 1.8.-.-, 1.2.99.-, 1.17.1.9, 1.2.7.12, 1.2.99.5
- UniProt
- Q2FKZ1, Q2FKZ0, Q2FME3, Q2FKZ3, Q2FKZ2, Q2FRK1, Q2FRL8, Q2FKZ5, Q2FRL9, Q2FRF6, Q2FKZ4, Q2FRM0
- Ligands
- SF4, FAD, 9S8, MGD, FES, ZN, MO
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 13 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Cob--com heterodisulfide reductase iron-sulfur subunit a (EC 1.8.-.-) | protein | 662 | 30% helix, 25% strand | Q2FKZ1 |
| F, f | F420-non-reducing hydrogenase subunit D | protein | 137 | 49% helix, 15% strand | Q2FKZ0 |
| E, e | Formate dehydrogenase, beta subunit (F420) (EC 1.2.99.-) | protein | 411 | 42% helix, 15% strand | Q2FME3 |
| C, c | Cob--com heterodisulfide reductase subunit C | protein | 189 | 57% helix, 1% strand | Q2FKZ3 |
| B, b | Cob--com heterodisulfide reductase subunit B | protein | 296 | 50% helix, 11% strand | Q2FKZ2 |
| D, d | Formate dehydrogenase (EC 1.17.1.9) | protein | 549 | 34% helix, 14% strand | Q2FRK1 |
| I, i | Formylmethanofuran dehydrogenase (EC 1.2.7.12) | protein | 264 | 3% helix, 29% strand | Q2FRL8 |
| L, l | Formylmethanofuran dehydrogenase, subunit G (EC 1.2.99.5) | protein | 79 | 10% helix, 20% strand | Q2FKZ5 |
| G, g | Formylmethanofuran dehydrogenase, subunit a (EC 1.2.99.5) | protein | 568 | 35% helix, 20% strand | Q2FRL9 |
| J, j | Formylmethanofuran dehydrogenase, subunit D (EC 1.2.99.5) | protein | 131 | 27% helix, 24% strand | Q2FRF6 |
| M, m | Formylmethanofuran dehydrogenase, subunit F (EC 1.2.99.5) | protein | 65 | 17% helix, 22% strand | Q2FKZ4 |
| K, k | Formylmethanofuran dehydrogenase, subunit F (EC 1.2.99.5) | protein | 321 | 16% helix, 21% strand | Q2FKZ4 |
| H, h | Formylmethanofuran dehydrogenase, subunit B (EC 1.2.99.5) | protein | 438 | 39% helix, 19% strand | Q2FRM0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 48 copies · chains A, E, C, D, L, K, M, H, a, e, c, d, l, k, m, h
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, a, E, e
- 9S8 · Non-cubane [4Fe-4S]-cluster · ligand · 4 copies · chains C, B, c, b
- MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 4 copies · chains J, H, j, h
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains F, f
- ZN · Zinc ion · metal · 4 copies · chains G, g
- MO · Molybdenum atom · metal · 2 copies · chains H, 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 | 692 | 0.88 | 0.93 | 87 | MO, MGD |
| 2 | 711 | 0.88 | 0.92 | 87 | MO, MGD |
| 3 | 258 | 0.81 | 0.93 | 58 | empty |
| 4 | 502 | 0.81 | 0.88 | 60 | FAD |
| 5 | 694 | 0.80 | 0.84 | 79 | FAD |
Interfaces
56 interfaces between chains.
- A–a · 3429 Ų buried · 36 hydrogen bonds · protein-protein
- C–B · 2764 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 2760 Ų buried · 40 hydrogen bonds · protein-protein
- c–b · 2758 Ų buried · 36 hydrogen bonds · protein-protein
- g–h · 2749 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 disulfide, 2 modified (covalent ligand, disulfide, carboxylation).
Compared structures
- 7BKC · Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase… · the same entry in another collection · chain F against F, 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 Q2FKZ1
- Every structure of UniProt Q2FKZ0
- Every structure of UniProt Q2FME3
- Every structure of UniProt Q2FKZ3
- Every structure of UniProt Q2FKZ2
- Every structure of UniProt Q2FRK1
- Every structure of UniProt Q2FRL8
- Every structure of UniProt Q2FKZ5
- Every structure of UniProt Q2FRL9
- Every structure of UniProt Q2FRF6
- Every structure of UniProt Q2FKZ4
- Every structure of UniProt Q2FRM0
- Elsewhere: RCSB PDB 7BKC · PDBe 7BKC · UniProt Q2FKZ1 · UniProt Q2FKZ0 · UniProt Q2FME3 · UniProt Q2FKZ3 · UniProt Q2FKZ2 · UniProt Q2FRK1 · UniProt Q2FRL8 · UniProt Q2FKZ5 · UniProt Q2FRL9 · UniProt Q2FRF6 · UniProt Q2FKZ4 · UniProt Q2FRM0
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