Research workbench
Tungsten-containing formylmethanofuran dehydrogenase from methanothermobacter wolfeii, orthorhombic form at 1.9 a
Analyse Tungsten-containing formylmethanofuran dehydrogenase from methanothermobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T5I
- Type
- protein
- Length
- 3,622 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tungsten formylmethanofuran dehydrogenase subunit fwda; Tungsten formylmethanofuran…
- EC
- 1.2.99.5
- Ligands
- SF4, MGD, K, NA, ZN, MG, W, CA, H2S
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 9 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Tungsten formylmethanofuran dehydrogenase subunit fwda | protein | 569 | 37% helix, 22% strand | — |
| B | Tungsten formylmethanofuran dehydrogenase subunit B | protein | 430 | 38% helix, 22% strand | — |
| C, K | Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C (EC 1.2.99.5) | protein | 269 | 7% helix, 36% strand | — |
| D, L | Tungsten formylmethanofuran dehydrogenase subunit fwdd | protein | 130 | 26% helix, 30% strand | — |
| F | Tungsten formylmethanofuran dehydrogenase subunit fwdf | protein | 335 | 20% helix, 27% strand | — |
| G | Tungsten formylmethanofuran dehydrogenase subunit fwdg | protein | 80 | 33% helix, 23% strand | — |
| J | Tungsten formylmethanofuran dehydrogenase subunit B | protein | 431 | 39% helix, 22% strand | — |
| N | Tungsten formylmethanofuran dehydrogenase subunit fwdf | protein | 329 | 20% helix, 25% strand | — |
| P | Tungsten formylmethanofuran dehydrogenase subunit fwdg | protein | 81 | 32% helix, 22% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 22 copies · chains B, F, G, J, N, P
- 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 B, D, J, L
- K · Potassium ion · metal · 18 copies · chains A, B, D, F, G, I, J, L, N, P
- NA · Sodium ion · metal · 5 copies · chains A, I, L
- ZN · Zinc ion · metal · 4 copies · chains A, I
- MG · Magnesium ion · metal · 2 copies · chains A, B, I, J
- W · Tungsten ion · metal · 2 copies · chains B, D, J, L
- CA · Calcium ion · metal · 2 copies · chains B, C, J, K
- H2S · Hydrosulfuric acid · ion · 2 copies · chains B, J
- GOL · Glycerol · additive · 9 copies · chains A, C, B, I, K, J, N
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 | 641 | 0.87 | 0.91 | 99 | W, MGD, H2S, K |
| 2 | 664 | 0.87 | 0.91 | 97 | W, MGD, H2S, K |
| 3 | 105 | 0.79 | 0.98 | 36 | empty |
| 4 | 96 | 0.77 | 0.98 | 35 | empty |
| 5 | 185 | 0.64 | 0.84 | 34 | GOL |
Interfaces
26 interfaces between chains.
- B–D · 2679 Ų buried · 41 hydrogen bonds · protein-protein
- J–L · 2657 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2569 Ų buried · 60 hydrogen bonds · protein-protein
- I–J · 2545 Ų buried · 59 hydrogen bonds · protein-protein
- J–K · 1986 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 5T5I · Tungsten-containing formylmethanofuran dehydrogenase from methanothermobacter wolfeii… · the same entry in another collection · chain I against I, 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 5T5I · PDBe 5T5I
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