MolNFT v1 · #173512 · protein
Crystal structure of the ethyl-coenzyme M reductase from candidatus ethanoperedens thermophilum gassed with xenon
7B2C · Ethyl-coenzyme M reductase alpha subunit: “Crystal structure of the ethyl-coenzyme M reductase from candidatus ethanoperedens thermophilum gassed with…”. X-ray diffraction, 9 ligands (USN, TP7, COM), 20 pockets (best druggability…
- PDB
- 7B2C
- Type
- protein
- Length
- 2,646 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ethyl-coenzyme M reductase alpha subunit; Ethyl-coenzyme M reductase beta subunit…
- EC
- 2.8.4.1
- Ligands
- USN, TP7, COM, UWT, K, NA, MG, XE, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ethyl-coenzyme M reductase alpha subunit (EC 2.8.4.1) | protein | 591 | 53% helix, 5% strand | — |
| B, E | Ethyl-coenzyme M reductase beta subunit (EC 2.8.4.1) | protein | 466 | 53% helix, 9% strand | — |
| C, F | Ethyl-coenzyme M reductase gamma subunit (EC 2.8.4.1) | protein | 265 | 33% helix, 18% strand | — |
| D | Ethyl-coenzyme M reductase alpha subunit (EC 2.8.4.1) | protein | 593 | 53% helix, 6% strand | — |
Ligands and binding sites
- USN · Dimethylated-F430 cofactor · ligand · 2 copies · chains A, B, C, D, E, F
- TP7 · Coenzyme B · ligand · 2 copies · chains A, B, D, E
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains A, B, C, D, E, F
- UWT · (2R)-2-[(2S)-2-[(2S)-2-oxidanylpropoxy]propoxy]propan-1-ol · ligand · 2 copies · chains C, D, F
- K · Potassium ion · metal · 17 copies · chains A, B, E, C, D, F
- NA · Sodium ion · metal · 5 copies · chains A, E, C, D, B
- MG · Magnesium ion · metal · chains A, D
- XE · Xenon · ion · 16 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 5 copies · chains B, E
- GOL · Glycerol · additive · 6 copies · chains A, C, E, B, D, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.88 | 0.89 | 115 | TP7, XE, CL, K, USN, COM |
| 2 | 1193 | 0.88 | 0.89 | 114 | USN, TP7, COM, XE, CL, K |
| 3 | 223 | 0.56 | 0.78 | 36 | GOL |
| 4 | 91 | 0.55 | 0.86 | 31 | empty |
| 5 | 169 | 0.55 | 0.80 | 35 | K |
Interfaces
14 interfaces between chains.
- A–D · 5245 Ų buried · 94 hydrogen bonds · protein-protein
- B–D · 3034 Ų buried · 47 hydrogen bonds · protein-protein
- A–E · 3002 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 2997 Ų buried · 58 hydrogen bonds · protein-protein
- E–F · 2991 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (methylation, nonstandard).
Compared structures
- 7B2C · Crystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens… · the same entry in another collection · chain A against A, 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 7B2C · PDBe 7B2C
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