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Dihydrodipicolinate synthase (dhdps) from C.JEJUNI with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site in C2221 space group
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI with pyruvate bound in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KXH
- Type
- protein
- Length
- 1,777 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
- 3VN, MG
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 47% helix, 14% strand | Q9PPB4 |
| F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 47% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- 3VN · (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid · ligand · 3 copies · chains A, D, B, C, E, F
- MG · Magnesium ion · metal · 10 copies · chains A, D, B, C, F
- EDO · 1,2-ethanediol · additive · 12 copies · chains B, C, A, D, E, F
- ACT · Acetate ion · additive · 9 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 6 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.75 | 0.89 | 48 | 3VN, MG |
| 2 | 252 | 0.75 | 0.89 | 48 | 3VN, MG |
| 3 | 244 | 0.73 | 0.88 | 38 | 3VN, MG |
| 4 | 571 | 0.68 | 0.78 | 57 | empty |
| 5 | 205 | 0.54 | 0.78 | 27 | ACT |
Interfaces
6 interfaces between chains.
- A–D · 1527 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1508 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1502 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1010 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 993 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KXH · Dihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate bound in the active site… · 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 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 Q9PPB4
- Elsewhere: RCSB PDB 7KXH · PDBe 7KXH · UniProt Q9PPB4
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