MolNFT v1 · #76923 · protein
Crystal structure of dapa (PA1010) at 1.6 a resolution
3QZE · Dihydrodipicolinate synthase: “Crystal structure of dapa (PA1010) at 1.6 a resolution”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.75). MolNFT v1 #76923 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3QZE
- Type
- protein
- Length
- 1,161 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q9I4W3
- Ligands
- CL
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 291 | 51% helix, 14% strand | Q9I4W3 |
| B, C, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 290 | 49% helix, 14% strand | Q9I4W3 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.75 | 0.86 | 59 | empty |
| 2 | 402 | 0.74 | 0.84 | 62 | empty |
| 3 | 126 | 0.52 | 0.81 | 31 | CL |
| 4 | 129 | 0.48 | 0.79 | 25 | CL |
| 5 | 110 | 0.47 | 0.80 | 26 | CL |
Interfaces
2 interfaces between chains.
- C–D · 1587 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1579 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3QZE · Crystal Structure of DapA (PA1010) at 1.6 A resolution · the same entry in another collection · chain D against D, TM-score 1.00
- Q9I4W3 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9I4W3) · a predicted model of the same protein · chain B 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 Q9I4W3
- Elsewhere: RCSB PDB 3QZE · PDBe 3QZE · UniProt Q9I4W3
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