Research workbench
Crystal structure of a dtdp-4-dehydrorhamnose reductase, rfbd ortholog (CA_C2315) from clostridium acetobutylicum atcc 824 at 2.05 a resolution
Analyse Crystal structure of a dtdp-4-dehydrorhamnose reductase, rfbd ortholog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VL0
- Type
- protein
- Length
- 842 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-4-dehydrorhamnose reductase, rfbd ortholog
- UniProt
- Q97GQ1
- Ligands
- NAI, UNL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dtdp-4-dehydrorhamnose reductase, rfbd ortholog | protein | 281 | 43% helix, 20% strand | Q97GQ1 |
| B | Dtdp-4-dehydrorhamnose reductase, rfbd ortholog | protein | 280 | 45% helix, 19% strand | Q97GQ1 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 3 copies · chains A, B, C
- UNL · Unknown ligand · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.74 | 0.77 | 60 | empty |
| 2 | 671 | 0.71 | 0.78 | 58 | NAI |
| 3 | 622 | 0.70 | 0.78 | 61 | NAI |
| 4 | 620 | 0.69 | 0.77 | 63 | NAI |
| 5 | 54 | 0.33 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 790 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 789 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1VL0 · Crystal structure of a dtdp-4-dehydrorhamnose reductase, rfbd ortholog (CA_C2315) from… · 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 Q97GQ1
- Elsewhere: RCSB PDB 1VL0 · PDBe 1VL0 · UniProt Q97GQ1
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