Research workbench
Short chain dehydrogenase (scr) cryoem structure with NADP and ethyl 4-chloroacetoacetate
Analyse Short chain dehydrogenase (scr) cryoem structure with NADP and ethyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VYQ
- Type
- protein
- Length
- 1,120 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbonyl reductase
- EC
- 1.1.1.-
- UniProt
- B2KJ46
- Ligands
- NAP, 83I
- Pockets
- 10 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, G | Carbonyl reductase (EC 1.1.1.-) | protein | 280 | 41% helix, 11% strand | B2KJ46 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, F, G
- 83I · ethyl 4-chloranyl-3-oxidanylidene-butanoate · ligand · 4 copies · chains A, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.84 | 0.85 | 65 | empty |
| 2 | 572 | 0.76 | 0.83 | 69 | NAP, 83I |
| 3 | 529 | 0.75 | 0.83 | 66 | NAP, 83I |
| 4 | 491 | 0.75 | 0.84 | 53 | NAP, 83I |
| 5 | 504 | 0.75 | 0.83 | 63 | NAP, 83I |
Interfaces
6 interfaces between chains.
- A–B · 2727 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 2726 Ų buried · 32 hydrogen bonds · protein-protein
- A–G · 2250 Ų buried · 27 hydrogen bonds · protein-protein
- B–F · 2236 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 345 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7VYQ · Short chain dehydrogenase (SCR) cryoEM structure with NADP and ethyl 4-chloroacetoacetate · the same entry in another collection · chain G against G, 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 B2KJ46
- Elsewhere: RCSB PDB 7VYQ · PDBe 7VYQ · UniProt B2KJ46
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