MolNFT v1 · #61072 · protein
Crystal structure of dihydrodipicolinate synthase from methicillin- resistant staphylococcus aureus
3DAQ: “Crystal structure of dihydrodipicolinate synthase from methicillin- resistant staphylococcus aureus”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.78). MolNFT v1 #61072 on GenesisL1: 3D structure, binding sites…
- PDB
- 3DAQ
- Type
- protein
- Length
- 1,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q6GH13
- Ligands
- CL
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 292 | 50% helix, 14% strand | Q6GH13 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.78 | 0.86 | 60 | GOL |
| 2 | 483 | 0.77 | 0.85 | 60 | GOL |
| 3 | 591 | 0.76 | 0.82 | 66 | GOL |
| 4 | 431 | 0.73 | 0.83 | 36 | GOL |
| 5 | 315 | 0.67 | 0.82 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1758 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1746 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 520 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 206 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3DAQ · Crystal structure of dihydrodipicolinate synthase from methicillin-resistant… · the same entry in another collection · chain D against D, TM-score 1.00
- Q6GH13 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q6GH13) · a predicted model of the same protein · chain C 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 Q6GH13
- Elsewhere: RCSB PDB 3DAQ · PDBe 3DAQ · UniProt Q6GH13
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