Research workbench
1.63 ångström resolution crystal structure of dehydrogenase (mvim) from clostridium difficile.
Analyse 1.63 ångström resolution crystal structure of dehydrogenase (mvim) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UUW
- Type
- protein
- Length
- 1,213 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase with NAD(P)-binding rossmann-fold domain
- UniProt
- Q180U8
- Ligands
- CL
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative oxidoreductase with NAD(P)-binding rossmann-fold domain | protein | 304 | 39% helix, 27% strand | Q180U8 |
| B, C, D | Putative oxidoreductase with NAD(P)-binding rossmann-fold domain | protein | 303 | 40% helix, 28% strand | Q180U8 |
Ligands and binding sites
- CL · Chloride ion · ion · 13 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.87 | 0.91 | 148 | PEG |
| 2 | 263 | 0.80 | 0.92 | 52 | PEG, 1PE |
| 3 | 206 | 0.74 | 0.90 | 42 | empty |
| 4 | 396 | 0.68 | 0.81 | 40 | CL |
| 5 | 390 | 0.68 | 0.80 | 42 | CL |
Interfaces
6 interfaces between chains.
- A–B · 1278 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1269 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1226 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1198 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 250 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3UUW · 1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM) from Clostridium… · 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
- Every structure of UniProt Q180U8
- Elsewhere: RCSB PDB 3UUW · PDBe 3UUW · UniProt Q180U8
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