MolNFT v1 · #134860 · protein
Crystal structure of a putative dehydrogenase from burkholderia cenocepacia with bound NADP
5THK: “Crystal structure of a putative dehydrogenase from burkholderia cenocepacia with bound NADP”. X-ray diffraction, 2 ligands (NAP, MG), 19 pockets (best druggability 0.81). MolNFT v1 #134860 on GenesisL1: 3D structure, binding sites…
- PDB
- 5THK
- Type
- protein
- Length
- 2,056 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dehydrogenase
- UniProt
- B4E8W7
- Ligands
- NAP, MG
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative dehydrogenase | protein | 255 | 49% helix, 16% strand | B4E8W7 |
| B | Putative dehydrogenase | protein | 257 | 49% helix, 18% strand | B4E8W7 |
| D, E, F, H | Putative dehydrogenase | protein | 256 | 49% helix, 16% strand | B4E8W7 |
| G | Putative dehydrogenase | protein | 265 | 48% helix, 15% strand | B4E8W7 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 2 copies · chains C, G
- 1PE · Pentaethylene glycol · additive · 2 copies · chains C, A, H
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 | 786 | 0.81 | 0.84 | 83 | NAP |
| 2 | 1059 | 0.81 | 0.82 | 100 | empty |
| 3 | 1096 | 0.80 | 0.81 | 102 | 1PE |
| 4 | 344 | 0.78 | 0.88 | 46 | NAP |
| 5 | 384 | 0.77 | 0.87 | 47 | NAP |
Interfaces
15 interfaces between chains.
- D–G · 2016 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1873 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1867 Ų buried · 25 hydrogen bonds · protein-protein
- C–G · 1866 Ų buried · 24 hydrogen bonds · protein-protein
- F–H · 1858 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5THK · Crystal Structure of a Putative Dehydrogenase from Burkholderia cenocepacia with bound… · 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 B4E8W7
- Elsewhere: RCSB PDB 5THK · PDBe 5THK · UniProt B4E8W7
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