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Crystal structure of short-chain DEHYDROGENASE/REDUCTASE sdr from mycobacterium smegmatis
Analyse Crystal structure of short-chain DEHYDROGENASE/REDUCTASE sdr from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PK0
- Type
- protein
- Length
- 1,043 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- A0QQJ6
- Ligands
- CA, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 260 | 47% helix, 15% strand | A0QQJ6 |
| B, C | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 262 | 47% helix, 15% strand | A0QQJ6 |
| D | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 259 | 47% helix, 15% strand | A0QQJ6 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.70 | 0.79 | 49 | GOL |
| 2 | 487 | 0.70 | 0.80 | 45 | PEG, GOL |
| 3 | 541 | 0.69 | 0.79 | 49 | GOL |
| 4 | 528 | 0.69 | 0.79 | 46 | GOL |
Interfaces
2 interfaces between chains.
- B–D · 1548 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1542 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3PK0 · Crystal structure of Short-chain dehydrogenase/reductase SDR from Mycobacterium smegmatis · 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 A0QQJ6
- Elsewhere: RCSB PDB 3PK0 · PDBe 3PK0 · UniProt A0QQJ6
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