MolNFT v1 · #165577 · protein
Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, N84A mutant with pyruvate bound in the active site
6TZU · 4-hydroxy-tetrahydrodipicolinate synthase: “Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, N84A mutant with pyruvate bound in the active site”. X-ray diffraction, 1 ligand (MG), 14 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 6TZU
- Type
- protein
- Length
- 1,795 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- Q9PPB4
- Ligands
- MG
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 48% helix, 14% strand | Q9PPB4 |
| B | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 304 | 47% helix, 13% strand | Q9PPB4 |
| D | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 306 | 46% helix, 13% strand | Q9PPB4 |
| E | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 47% helix, 14% strand | Q9PPB4 |
| F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 48% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, E, F
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B, F, D, E
- ACT · Acetate ion · additive · 16 copies · chains A, D, B, C, F, E
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, D, F
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, C, E
- GOL · Glycerol · additive · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.76 | 0.86 | 51 | empty |
| 2 | 411 | 0.76 | 0.85 | 50 | empty |
| 3 | 347 | 0.75 | 0.86 | 51 | empty |
| 4 | 203 | 0.54 | 0.78 | 34 | ACT, PEG |
| 5 | 176 | 0.54 | 0.79 | 35 | EDO |
Interfaces
6 interfaces between chains.
- B–C · 1488 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1474 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1466 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 996 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 994 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6TZU · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant with pyruvate bound in… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9PPB4 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9PPB4) · a predicted model of the same protein · 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 Q9PPB4
- Elsewhere: RCSB PDB 6TZU · PDBe 6TZU · UniProt Q9PPB4
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