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Methyl-coenzyme M reductase II from methanothermobacter marburgensis at 2.15 a resolution
Analyse Methyl-coenzyme M reductase II from methanothermobacter marburgensis at 2.15 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A8R
- Type
- protein
- Length
- 5,008 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- METHANOTHERMOBACTER MARBURGENSIS
- Molecule
- Methyl-coenzyme M reductase II subunit alpha; Methyl-coenzyme M reductase II subunit…
- EC
- 2.8.4.1
- UniProt
- P58815, D9PXZ6, P58816
- Ligands
- COM, TP7, F43, K
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · resolution 2.15 · 6 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Methyl-coenzyme M reductase II subunit alpha (EC 2.8.4.1) | protein | 548 | 54% helix, 5% strand | P58815 |
| B, E, H, K | Methyl-coenzyme M reductase II subunit gamma (EC 2.8.4.1) | protein | 442 | 56% helix, 9% strand | D9PXZ6 |
| C | Methyl-coenzyme M reductase II, subunit beta (EC 2.8.4.1) | protein | 262 | 34% helix, 16% strand | P58816 |
| F | Methyl-coenzyme M reductase II, subunit beta (EC 2.8.4.1) | protein | 261 | 34% helix, 17% strand | P58816 |
| I | Methyl-coenzyme M reductase II, subunit beta (EC 2.8.4.1) | protein | 262 | 34% helix, 16% strand | P58816 |
| L | Methyl-coenzyme M reductase II, subunit beta (EC 2.8.4.1) | protein | 263 | 34% helix, 16% strand | P58816 |
Ligands and binding sites
- COM · 1-thioethanesulfonic acid · ligand · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- TP7 · Coenzyme B · ligand · 4 copies · chains A, D, E, B, G, H, J, K
- F43 · Factor 430 · ligand · 4 copies · chains A, D, E, F, B, C, G, H, I, J, K, L
- K · Potassium ion · metal · 7 copies · chains A, D, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.90 | 0.91 | 125 | COM, TP7, F43 |
| 2 | 1156 | 0.88 | 0.90 | 134 | COM, TP7, F43 |
| 3 | 1199 | 0.88 | 0.89 | 128 | TP7, F43, COM |
| 4 | 1177 | 0.88 | 0.89 | 121 | COM, TP7, F43 |
| 5 | 421 | 0.72 | 0.83 | 40 | empty |
Interfaces
34 interfaces between chains.
- A–D · 5232 Ų buried · 80 hydrogen bonds · protein-protein
- G–J · 5229 Ų buried · 80 hydrogen bonds · protein-protein
- H–I · 3045 Ų buried · 51 hydrogen bonds · protein-protein
- K–L · 3039 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 3011 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (methylation, nonstandard).
Compared structures
- 5A8R · Methyl-coenzyme M reductase II from methanothermobacter marburgensis at 2.15 a resolution · the same entry in another collection · chain L against L, 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 P58815
- Every structure of UniProt D9PXZ6
- Every structure of UniProt P58816
- Elsewhere: RCSB PDB 5A8R · PDBe 5A8R · UniProt P58815 · UniProt D9PXZ6 · UniProt P58816
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