Research workbench
Crystal structure of dihydrodipicolinate reductase (TM1520) from thermotoga maritima at 2.27 a resolution
Analyse Crystal structure of dihydrodipicolinate reductase (TM1520) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VM6
- Type
- protein
- Length
- 865 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate reductase
- EC
- 1.3.1.26
- UniProt
- Q9X1K8
- Ligands
- NAD
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 215 | 37% helix, 28% strand | Q9X1K8 |
| B | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 218 | 37% helix, 28% strand | Q9X1K8 |
| C | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 215 | 38% helix, 27% strand | Q9X1K8 |
| D | Dihydrodipicolinate reductase (EC 1.3.1.26) | protein | 217 | 37% helix, 28% strand | Q9X1K8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 12 copies · chains A, B, D, C
- PG4 · Tetraethylene glycol · additive · 4 copies · chains B, C
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.87 | 0.93 | 68 | ACT |
| 2 | 328 | 0.74 | 0.86 | 40 | ACT, NAD |
| 3 | 362 | 0.73 | 0.84 | 41 | ACT, NAD |
| 4 | 357 | 0.73 | 0.85 | 42 | ACT, NAD |
| 5 | 500 | 0.63 | 0.76 | 50 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1170 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1053 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 829 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 816 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 282 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1VM6 · Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9X1K8 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate reductase (Q9X1K8) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9X1K8
- Elsewhere: RCSB PDB 1VM6 · PDBe 1VM6 · UniProt Q9X1K8
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