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Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, Y110F mutant with R,R-bislysine bound at the allosteric site at 2.7 ångström
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, Y110F mutant with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M06
- Type
- protein
- Length
- 1,185 residues
- Chains
- 4
- 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
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 48% helix, 14% strand | Q9PPB4 |
| D | 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 · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.78 | 0.84 | 62 | 3VN, MG, PEG |
| 2 | 603 | 0.77 | 0.83 | 63 | PGE, 3VN, PEG |
| 3 | 216 | 0.60 | 0.81 | 33 | empty |
| 4 | 191 | 0.54 | 0.79 | 28 | MG |
| 5 | 190 | 0.53 | 0.78 | 26 | MG |
Interfaces
4 interfaces between chains.
- C–D · 1387 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1377 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1032 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1024 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7M06 · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, Y110F mutant with R,R-bislysine bound… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9PPB4 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9PPB4) · 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 Q9PPB4
- Elsewhere: RCSB PDB 7M06 · PDBe 7M06 · UniProt Q9PPB4
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