Research workbench
Crystal structure of a putative dehydrogenase from xanthomonas campestris
Analyse Crystal structure of a putative dehydrogenase from xanthomonas campestris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E03
- Type
- protein
- Length
- 810 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain dehydrogenase
- UniProt
- Q8P5Q1
- Ligands
- CA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short chain dehydrogenase | protein | 267 | 45% helix, 15% strand | Q8P5Q1 |
| B | Short chain dehydrogenase | protein | 271 | 46% helix, 15% strand | Q8P5Q1 |
| C | Short chain dehydrogenase | protein | 272 | 46% helix, 14% strand | Q8P5Q1 |
Ligands and binding sites
- CA · Calcium ion · metal · 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 | 390 | 0.78 | 0.87 | 43 | empty |
| 2 | 1139 | 0.78 | 0.80 | 117 | empty |
| 3 | 495 | 0.76 | 0.84 | 44 | empty |
| 4 | 465 | 0.67 | 0.79 | 42 | empty |
| 5 | 105 | 0.45 | 0.78 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 408 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 336 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 229 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 3E03 · Crystal structure of a putative dehydrogenase from Xanthomonas campestris · 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
- Every structure of UniProt Q8P5Q1
- Elsewhere: RCSB PDB 3E03 · PDBe 3E03 · UniProt Q8P5Q1
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