MolNFT v1 · #64819 · protein
Crystal structure of short-chain dehydrogenase from pseudomonas syringae
3GEM · Short chain dehydrogenase: “Crystal structure of short-chain dehydrogenase from pseudomonas syringae”. X-ray diffraction, 11 pockets (best druggability 0.79). MolNFT v1 #64819 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3GEM
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain dehydrogenase
- UniProt
- Q48MN0
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short chain dehydrogenase | protein | 217 | 46% helix, 15% strand | Q48MN0 |
| B | Short chain dehydrogenase | protein | 221 | 46% helix, 14% strand | Q48MN0 |
| C | Short chain dehydrogenase | protein | 224 | 50% helix, 14% strand | Q48MN0 |
| D | Short chain dehydrogenase | protein | 214 | 51% helix, 15% strand | Q48MN0 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.79 | 0.81 | 72 | empty |
| 2 | 121 | 0.63 | 0.87 | 22 | empty |
| 3 | 235 | 0.59 | 0.80 | 37 | empty |
| 4 | 175 | 0.56 | 0.81 | 28 | empty |
| 5 | 133 | 0.53 | 0.81 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1379 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1366 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1270 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1170 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 149 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3GEM · Crystal structure of short-chain dehydrogenase from Pseudomonas syringae · 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 Q48MN0
- Elsewhere: RCSB PDB 3GEM · PDBe 3GEM · UniProt Q48MN0
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