MolNFT v1 · #72492 · protein
Crystal structure of a putative dihydrodipicolinate synthetase from pseudomonas aeruginosa
3NA8: “Crystal structure of a putative dihydrodipicolinate synthetase from pseudomonas aeruginosa”. X-ray diffraction, 2 ligands (MLT, MG), 7 pockets (best druggability 0.83). MolNFT v1 #72492 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3NA8
- Type
- protein
- Length
- 1,162 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dihydrodipicolinate synthetase
- EC
- 4.2.1.52
- UniProt
- Q9I6R5
- Ligands
- MLT, MG
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative dihydrodipicolinate synthetase (EC 4.2.1.52) | protein | 291 | 54% helix, 13% strand | Q9I6R5 |
| B | Putative dihydrodipicolinate synthetase (EC 4.2.1.52) | protein | 290 | 53% helix, 13% strand | Q9I6R5 |
| D | Putative dihydrodipicolinate synthetase (EC 4.2.1.52) | protein | 290 | 53% helix, 13% strand | Q9I6R5 |
Ligands and binding sites
- MLT · D-malate · ligand · 3 copies · chains A, C, D
- MG · Magnesium ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.83 | 0.84 | 124 | empty |
| 2 | 1061 | 0.83 | 0.84 | 127 | empty |
| 3 | 69 | 0.39 | 0.79 | 17 | empty |
| 4 | 118 | 0.37 | 0.73 | 23 | empty |
| 5 | 82 | 0.32 | 0.74 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1257 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1238 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1046 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1034 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 1 covalent (engineered, oxidation, covalent ligand).
Compared structures
- 3NA8 · Crystal Structure of a putative dihydrodipicolinate synthetase from Pseudomonas aeruginosa · the same entry in another collection · chain A 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 Q9I6R5
- Elsewhere: RCSB PDB 3NA8 · PDBe 3NA8 · UniProt Q9I6R5
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