Research workbench
Crystal structure of the ethyl-coenzyme M reductase from candidatus ethanoperedens thermophilum at 0.994-a resolution
Analyse Crystal structure of the ethyl-coenzyme M reductase from candidatus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B1S
- 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
- TP7, USN, COM, UUT, K, MN, CL
- Pockets
- 19 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 51% 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 | 54% 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, 17% strand | — |
| D | Ethyl-coenzyme M reductase alpha subunit (EC 2.8.4.1) | protein | 593 | 54% helix, 5% strand | — |
Ligands and binding sites
- TP7 · Coenzyme B · ligand · 2 copies · chains A, B, D, E
- USN · Dimethylated-F430 cofactor · ligand · 2 copies · chains A, B, C, D, E, F
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains A, B, C, D, E, F
- UUT · (2S)-2-{[(2S)-2-{[(2S)-2-hydroxypropyl]oxy}propyl]oxy}propan-1-ol · ligand · 2 copies · chains C, F
- K · Potassium ion · metal · 4 copies · chains A, E, C, D
- MN · Manganese (II) ion · metal · chains A, D
- CL · Chloride ion · ion · 6 copies · chains B, C, E, F
- GOL · Glycerol · additive · 4 copies · chains A, D, E, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.90 | 0.92 | 104 | USN, TP7, CL, COM |
| 2 | 1035 | 0.90 | 0.91 | 111 | TP7, CL, USN, COM |
| 3 | 322 | 0.62 | 0.79 | 50 | K |
| 4 | 196 | 0.61 | 0.82 | 42 | CL |
| 5 | 277 | 0.60 | 0.79 | 42 | empty |
Interfaces
14 interfaces between chains.
- A–D · 5213 Ų buried · 92 hydrogen bonds · protein-protein
- A–E · 3043 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 3028 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 2999 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 2991 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (methylation, nonstandard).
Compared structures
- 7B1S · Crystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens… · the same entry in another collection · chain B against B, 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 7B1S · PDBe 7B1S
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