Research workbench
NAD-soaked holo-methanol dehydrogenase (mdh) from methylococcus capsulatus (bath)
Analyse NAD-soaked holo-methanol dehydrogenase (mdh) from methylococcus capsulatus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CFX
- Type
- protein
- Length
- 5,152 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methanol dehydrogenase protein, large subunit; Methanol dehydrogenase [cytochrome C]…
- EC
- 1.1.2.7
- UniProt
- Q60AR6, Q60AR3
- Ligands
- PQQ, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, A, B, G, H, M, N | Methanol dehydrogenase protein, large subunit | protein | 573 | 10% helix, 37% strand | Q60AR6 |
| K, L, E, F, I, J, O, P | Methanol dehydrogenase [cytochrome C] subunit 2 (EC 1.1.2.7) | protein | 71 | 39% helix, 3% strand | Q60AR3 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · 8 copies · chains C, D, A, B, G, H, M, N
- CA · Calcium ion · metal · 8 copies · chains C, D, A, B, G, H, M, 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 | 121 | 0.81 | 0.99 | 30 | CA, PQQ |
| 2 | 131 | 0.81 | 0.98 | 28 | CA, PQQ |
| 3 | 124 | 0.81 | 0.98 | 31 | CA, PQQ |
| 4 | 128 | 0.80 | 0.98 | 31 | CA, PQQ |
| 5 | 114 | 0.80 | 0.98 | 30 | CA, PQQ |
Interfaces
20 interfaces between chains.
- B–F · 2071 Ų buried · 30 hydrogen bonds · protein-protein
- N–P · 2061 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 2057 Ų buried · 33 hydrogen bonds · protein-protein
- H–J · 2050 Ų buried · 29 hydrogen bonds · protein-protein
- C–K · 2045 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 7CFX · NAD-soaked Holo-methanol dehydrogenase (MDH) from Methylococcus capsulatus (Bath) · the same entry in another collection · chain C against C, 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 Q60AR6
- Every structure of UniProt Q60AR3
- Elsewhere: RCSB PDB 7CFX · PDBe 7CFX · UniProt Q60AR6 · UniProt Q60AR3
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