MolNFT v1 · #136413 · protein
Structure of dihydrodipicolinate reductase from vibrio vulnificus bound to NADH and 2,6 pyridine dicarboxylic acid with intact polyhistidine tag
5US6 · 4-hydroxy-tetrahydrodipicolinate reductase: “Structure of dihydrodipicolinate reductase from vibrio vulnificus bound to NADH and 2,6 pyridine dicarboxylic…”. X-ray diffraction, 3 ligands (NAD, PDC, SO4), 20 pockets (best…
- 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
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