MolNFT v1 · #55864 · protein
Crystal structure of dihyrodipicolinate synthase (dapa)
2YXG · Dihydrodipicolinate synthase: “Crystal structure of dihyrodipicolinate synthase (dapa)”. X-ray diffraction, 8 pockets (best druggability 0.79). MolNFT v1 #55864 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2YXG
- Type
- protein
- Length
- 1,153 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q57695
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 289 | 51% helix, 15% strand | Q57695 |
| B, C, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 288 | 50% helix, 15% strand | Q57695 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.79 | 0.83 | 93 | empty |
| 2 | 474 | 0.74 | 0.83 | 55 | empty |
| 3 | 206 | 0.63 | 0.83 | 27 | empty |
| 4 | 220 | 0.63 | 0.83 | 31 | empty |
| 5 | 220 | 0.62 | 0.82 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1449 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1443 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 990 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 987 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2YXG · Crystal structure of Dihyrodipicolinate Synthase (dapA) · the same entry in another collection · chain D against D, TM-score 1.00
- Q57695 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q57695) · a predicted model of the same protein · chain D 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 Q57695
- Elsewhere: RCSB PDB 2YXG · PDBe 2YXG · UniProt Q57695
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