MolNFT v1 · #136982 · protein
Crystal structure of short-chain DEHYDROGENASE/REDUCTASE sdr from burkholderia phymatum in complex with NADP
5VA8: “Crystal structure of short-chain DEHYDROGENASE/REDUCTASE sdr from burkholderia phymatum in complex with NADP”. X-ray diffraction, 2 ligands (NAP, TCE), 5 pockets (best druggability 0.76). MolNFT v1 #136982 on GenesisL1: 3D…
- PDB
- 5VA8
- Type
- protein
- Length
- 1,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- B2JE32
- Ligands
- NAP, TCE
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 261 | 50% helix, 16% strand | B2JE32 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- TCE · 3,3',3''-phosphanetriyltripropanoic acid · ligand · 4 copies · chains A, B, C, D
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 3 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.76 | 0.97 | 21 | empty |
| 2 | 575 | 0.72 | 0.80 | 66 | NAP, TCE |
| 3 | 762 | 0.72 | 0.78 | 75 | NAP, TCE |
| 4 | 606 | 0.72 | 0.79 | 67 | NAP, TCE |
| 5 | 747 | 0.71 | 0.77 | 69 | NAP, TCE |
Interfaces
6 interfaces between chains.
- A–B · 2150 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2141 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1433 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 1420 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 288 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5VA8 · Crystal Structure of Short-chain dehydrogenase/reductase SDR from Burkholderia phymatum… · 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 B2JE32
- Elsewhere: RCSB PDB 5VA8 · PDBe 5VA8 · UniProt B2JE32
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