MolNFT v1 · #135569 · protein
Crystal structure of a short chain dehydrogenase from burkholderia cenocepacia J2315 in complex with NADP
5U2W: “Crystal structure of a short chain dehydrogenase from burkholderia cenocepacia J2315 in complex with NADP”. X-ray diffraction, 1 ligand (NAP), 5 pockets (best druggability 0.86). MolNFT v1 #135569 on GenesisL1: 3D structure, binding…
- PDB
- 5U2W
- Type
- protein
- Length
- 981 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain dehydrogenase
- UniProt
- B4E730
- Ligands
- NAP
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short chain dehydrogenase | protein | 246 | 43% helix, 15% strand | B4E730 |
| B, C, D | Short chain dehydrogenase | protein | 245 | 44% helix, 15% strand | B4E730 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.86 | 0.87 | 81 | empty |
| 2 | 1128 | 0.82 | 0.83 | 140 | NAP, IMD |
| 3 | 1001 | 0.82 | 0.83 | 128 | NAP, IMD |
| 4 | 141 | 0.44 | 0.76 | 22 | empty |
| 5 | 132 | 0.43 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1621 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1567 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1490 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1439 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 267 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5U2W · Crystal structure of a Short chain dehydrogenase from Burkholderia cenocepacia J2315 in… · 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 B4E730
- Elsewhere: RCSB PDB 5U2W · PDBe 5U2W · UniProt B4E730
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