Research workbench
Crystal structure of a short-chain type DEHYDROGENASE/REDUCTASE from mycobacterium marinum
Analyse Crystal structure of a short-chain type DEHYDROGENASE/REDUCTASE from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TZQ
- Type
- protein
- Length
- 2,079 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain type DEHYDROGENASE/REDUCTASE
- EC
- 1.-.-.-
- UniProt
- B2HKN3
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Short-chain type DEHYDROGENASE/REDUCTASE (EC 1.-.-.-) | protein | 258 | 49% helix, 16% strand | B2HKN3 |
| A | Short-chain type DEHYDROGENASE/REDUCTASE (EC 1.-.-.-) | protein | 259 | 48% helix, 15% strand | B2HKN3 |
| D | Short-chain type DEHYDROGENASE/REDUCTASE (EC 1.-.-.-) | protein | 259 | 51% helix, 15% strand | B2HKN3 |
| C, F, H | Short-chain type DEHYDROGENASE/REDUCTASE (EC 1.-.-.-) | protein | 261 | 48% helix, 15% strand | B2HKN3 |
| E, G | Short-chain type DEHYDROGENASE/REDUCTASE (EC 1.-.-.-) | protein | 260 | 50% helix, 16% strand | B2HKN3 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains B, D, A, C, F, H, G, E
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, D, C, F, E, H, G
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, F, H, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.83 | 0.84 | 88 | PEG, EDO |
| 2 | 974 | 0.83 | 0.84 | 112 | PEG |
| 3 | 1087 | 0.83 | 0.84 | 83 | EDO, PEG |
| 4 | 434 | 0.78 | 0.86 | 49 | GOL |
| 5 | 523 | 0.76 | 0.83 | 50 | GOL |
Interfaces
15 interfaces between chains.
- A–D · 1751 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 1743 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1741 Ų buried · 24 hydrogen bonds · protein-protein
- E–H · 1740 Ų buried · 23 hydrogen bonds · protein-protein
- H–G · 1552 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3TZQ · Crystal structure of a short-chain type dehydrogenase/reductase from Mycobacterium marinum · 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 B2HKN3
- Elsewhere: RCSB PDB 3TZQ · PDBe 3TZQ · UniProt B2HKN3
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