Research workbench
Structure of dihydrodipicolinate reductase from vibrio vulnificus bound to NADH and 2,6 pyridine dicarboxylic acid with intact polyhistidine tag
Analyse Structure of dihydrodipicolinate reductase from vibrio vulnificus bound to NADH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5US6
- Type
- protein
- Length
- 3,159 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate reductase
- EC
- 1.17.1.8
- UniProt
- Q8DEM0
- Ligands
- NAD, PDC, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 267 | 38% helix, 26% strand | Q8DEM0 |
| B, F | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 266 | 38% helix, 26% strand | Q8DEM0 |
| C, G, K | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 266 | 38% helix, 26% strand | Q8DEM0 |
| D | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 260 | 37% helix, 27% strand | Q8DEM0 |
| H | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 264 | 39% helix, 26% strand | Q8DEM0 |
| J | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 267 | 39% helix, 26% strand | Q8DEM0 |
| L | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 237 | 38% helix, 25% strand | Q8DEM0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 9 copies · chains A, B, C, E, F, G, I, J, K
- PDC · Pyridine-2,6-dicarboxylic acid · ligand · 9 copies · chains A, B, C, E, F, G, I, J, K
- SO4 · Sulfate ion · ion · 23 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 730 | 0.86 | 0.90 | 51 | empty |
| 2 | 726 | 0.86 | 0.90 | 51 | empty |
| 3 | 707 | 0.86 | 0.89 | 52 | empty |
| 4 | 1109 | 0.81 | 0.82 | 123 | NAD, PDC, SO4 |
| 5 | 1144 | 0.76 | 0.79 | 118 | NAD, PDC |
Interfaces
24 interfaces between chains.
- E–G · 1664 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1657 Ų buried · 34 hydrogen bonds · protein-protein
- F–H · 1646 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1645 Ų buried · 34 hydrogen bonds · protein-protein
- I–K · 1640 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 5US6 · Structure of Dihydrodipicolinate Reductase from Vibrio vulnificus Bound to NADH and 2,6… · the same entry in another collection · chain L against L, 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 Q8DEM0
- Elsewhere: RCSB PDB 5US6 · PDBe 5US6 · UniProt Q8DEM0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.