MolNFT v1 · #135795 · protein
Crystal structure of a gluconate 5-dehydrogenase from burkholderia cenocepacia J2315 in complex with NADP and tartrate
5U9P: “Crystal structure of a gluconate 5-dehydrogenase from burkholderia cenocepacia J2315 in complex with NADP and…”. X-ray diffraction, 1 ligand (NAP), 8 pockets (best druggability 0.86). MolNFT v1 #135795 on GenesisL1: 3D structure…
- PDB
- 5U9P
- Type
- protein
- Length
- 1,031 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gluconate 5-dehydrogenase
- EC
- 1.1.1.69
- UniProt
- B4EEX4
- Ligands
- NAP
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gluconate 5-dehydrogenase (EC 1.1.1.69) | protein | 258 | 54% helix, 14% strand | B4EEX4 |
| B | Gluconate 5-dehydrogenase (EC 1.1.1.69) | protein | 261 | 52% helix, 16% strand | B4EEX4 |
| C | Gluconate 5-dehydrogenase (EC 1.1.1.69) | protein | 255 | 54% helix, 16% strand | B4EEX4 |
| D | Gluconate 5-dehydrogenase (EC 1.1.1.69) | protein | 257 | 53% helix, 14% strand | B4EEX4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, D, C
- TLA · L(+)-tartaric acid · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.86 | 0.93 | 54 | empty |
| 2 | 314 | 0.74 | 0.86 | 44 | NAP, TLA |
| 3 | 306 | 0.73 | 0.86 | 41 | NAP, TLA |
| 4 | 313 | 0.72 | 0.85 | 42 | NAP, TLA |
| 5 | 304 | 0.72 | 0.85 | 41 | NAP, TLA |
Interfaces
6 interfaces between chains.
- B–C · 1913 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1764 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1582 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1580 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 453 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5U9P · Crystal structure of a gluconate 5-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 B4EEX4
- Elsewhere: RCSB PDB 5U9P · PDBe 5U9P · UniProt B4EEX4
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