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Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, N84D mutant with pyruvate bound in the active site
Analyse Dihydrodipicolinate synthase (dhdps) from C.JEJUNI, N84D 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
- 6U01
- 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
- A0A2U0QMK8
- Ligands
- MG
- Pockets
- 14 · best druggability 0.74
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 | 48% helix, 14% strand | A0A2U0QMK8 |
| F | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 297 | 47% helix, 14% strand | A0A2U0QMK8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains B, C, E, F
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, E, F
- ACT · Acetate ion · additive · 6 copies · chains B, C, D, E
- PGE · Triethylene glycol · additive · 4 copies · chains B, C, D, E
- PG4 · Tetraethylene glycol · additive · chains A
- GOL · Glycerol · additive · chains C, E
- PEG · Di(hydroxyethyl)ether · additive · chains F
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 | 383 | 0.74 | 0.85 | 52 | empty |
| 2 | 350 | 0.74 | 0.86 | 53 | empty |
| 3 | 349 | 0.73 | 0.85 | 52 | empty |
| 4 | 589 | 0.68 | 0.78 | 56 | GOL |
| 5 | 161 | 0.51 | 0.79 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1494 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1469 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1455 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1012 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 993 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 6U01 · Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in… · 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 A0A2U0QMK8
- Elsewhere: RCSB PDB 6U01 · PDBe 6U01 · UniProt A0A2U0QMK8
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