MolNFT v1 · #137168 · protein
Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from xanthobacter autotrophicus PY2 in complex with NADPH and mes.
5VG6 · D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding: “Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from xanthobacter autotrophicus PY2 in…”. X-ray diffraction, 1 ligand (NDP), 20 pockets (best…
- PDB
- 5VG6
- Type
- protein
- Length
- 2,992 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
- UniProt
- A7IIH0
- Ligands
- NDP
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding | protein | 314 | 35% helix, 18% strand | A7IIH0 |
| B, C, I, J | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding | protein | 315 | 35% helix, 18% strand | A7IIH0 |
| D | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding | protein | 308 | 36% helix, 18% strand | A7IIH0 |
| F | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding | protein | 312 | 35% helix, 17% strand | A7IIH0 |
| G, H | D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding | protein | 242 | 38% helix, 15% strand | A7IIH0 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 9 copies · chains A, J, B, C, D, E, F, I
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 | 725 | 0.81 | 0.85 | 89 | NDP, MES |
| 2 | 699 | 0.81 | 0.85 | 92 | NDP, MES |
| 3 | 1027 | 0.81 | 0.82 | 122 | NDP, MES |
| 4 | 599 | 0.80 | 0.85 | 83 | NDP, MES |
| 5 | 853 | 0.80 | 0.83 | 113 | NDP, MES |
Interfaces
21 interfaces between chains.
- E–I · 2241 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2177 Ų buried · 28 hydrogen bonds · protein-protein
- A–J · 2162 Ų buried · 28 hydrogen bonds · protein-protein
- F–G · 1986 Ų buried · 19 hydrogen bonds · protein-protein
- D–H · 1986 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5VG6 · Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter… · 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 A7IIH0
- Elsewhere: RCSB PDB 5VG6 · PDBe 5VG6 · UniProt A7IIH0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.