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Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H59A mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, H59A mutant with pyruvate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KM0
- Type
- protein
- Length
- 1,776 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 0.80
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 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 B, C, A, D, E, F
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, D, C
- ACT · Acetate ion · additive · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.80 | 0.86 | 61 | 3VN |
| 2 | 488 | 0.79 | 0.86 | 60 | PEG, 3VN |
| 3 | 377 | 0.78 | 0.88 | 52 | 3VN |
| 4 | 658 | 0.71 | 0.78 | 62 | empty |
| 5 | 200 | 0.53 | 0.78 | 24 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1475 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1470 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1451 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1026 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1013 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7KM0 · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59A 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 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 7KM0 · PDBe 7KM0 · UniProt Q9PPB4
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