Research workbench
Crystal structure of heterotetrameric human ketoacyl reductase complexed with NAD and NADP
Analyse Crystal structure of heterotetrameric human ketoacyl reductase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CQM
- Type
- protein
- Length
- 3,852 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estradiol 17-beta-dehydrogenase 8; Carbonyl reductase family member 4
- EC
- 1.1.1.62, 1.1.1.239, 1.1.1.100, 1.1.1.-
- UniProt
- Q92506, Q8N4T8
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 15 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62, 1.1.1.239, 1.1.1.100) | protein | 248 | 48% helix, 17% strand | Q92506 |
| B | Carbonyl reductase family member 4 (EC 1.1.1.100) | protein | 232 | 43% helix, 19% strand | Q8N4T8 |
| C | Carbonyl reductase family member 4 (EC 1.1.1.100) | protein | 232 | 48% helix, 18% strand | Q8N4T8 |
| D | Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62, 1.1.1.-, 1.1.1.239, 1.1.1.100) | protein | 248 | 46% helix, 17% strand | Q92506 |
| E, P | Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62, 1.1.1.239, 1.1.1.100) | protein | 248 | 49% helix, 17% strand | Q92506 |
| F | Carbonyl reductase family member 4 (EC 1.1.1.100) | protein | 241 | 50% helix, 17% strand | Q8N4T8 |
| G | Carbonyl reductase family member 4 (EC 1.1.1.100) | protein | 224 | 47% helix, 16% strand | Q8N4T8 |
| H | Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62, 1.1.1.239, 1.1.1.100) | protein | 249 | 47% helix, 16% strand | Q92506 |
| I | Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62, 1.1.1.239, 1.1.1.100) | protein | 249 | 48% helix, 17% strand | Q92506 |
| J | Carbonyl reductase family member 4 (EC 1.1.1.100) | protein | 240 | 47% helix, 17% strand | Q8N4T8 |
| K | Carbonyl reductase family member 4 (EC 1.1.1.100) | protein | 231 | 48% helix, 17% strand | Q8N4T8 |
| L | Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62, 1.1.1.239, 1.1.1.100) | protein | 246 | 48% helix, 17% strand | Q92506 |
| M | Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62, 1.1.1.239, 1.1.1.100) | protein | 249 | 50% helix, 16% strand | Q92506 |
| N | Carbonyl reductase family member 4 (EC 1.1.1.100) | protein | 232 | 47% helix, 17% strand | Q8N4T8 |
| O | Carbonyl reductase family member 4 (EC 1.1.1.100) | protein | 235 | 48% helix, 17% strand | Q8N4T8 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 16 copies · chains A, B, J, C, D, E, F, G, H, I, K, L, M, N, O, P
- EDO · 1,2-ethanediol · additive · 8 copies · chains D, B, E, F, I, L, J, M, P
- GOL · Glycerol · additive · 4 copies · chains A, D, E, H, I, L, M, P
- ACT · Acetate ion · additive · 3 copies · chains H, J, M, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.87 | 0.89 | 50 | GOL |
| 2 | 688 | 0.87 | 0.90 | 52 | GOL |
| 3 | 769 | 0.87 | 0.90 | 55 | GOL |
| 4 | 787 | 0.87 | 0.89 | 56 | GOL |
| 5 | 954 | 0.83 | 0.84 | 81 | empty |
Interfaces
35 interfaces between chains.
- B–C · 1722 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 1721 Ų buried · 28 hydrogen bonds · protein-protein
- I–L · 1708 Ų buried · 24 hydrogen bonds · protein-protein
- M–P · 1703 Ų buried · 27 hydrogen bonds · protein-protein
- J–K · 1700 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4CQM · Crystal structure of heterotetrameric human ketoacyl reductase complexed with NAD and NADP · the same entry in another collection · chain K against K, 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 Q92506
- Every structure of UniProt Q8N4T8
- Elsewhere: RCSB PDB 4CQM · PDBe 4CQM · UniProt Q92506 · UniProt Q8N4T8
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