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Dihydrodipicolinate synthase (dhdps) from C.JEJUNI with pyruvate bound in the active site in P1211 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
- 7L4B
- Type
- protein
- Length
- 3,550 residues
- Chains
- 12
- 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
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G, H, I, J, K, L | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 47% helix, 14% strand | Q9PPB4 |
| E | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 294 | 48% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, C, D, E, F, J
- PGE · Triethylene glycol · additive · 14 copies · chains A, B, C, D, E, G, F, H, I, J, K, L
- ACT · Acetate ion · additive · 3 copies · chains C, I, F, H, E, L
- EDO · 1,2-ethanediol · additive · chains J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.74 | 0.85 | 55 | empty |
| 2 | 334 | 0.74 | 0.86 | 54 | empty |
| 3 | 351 | 0.74 | 0.85 | 52 | empty |
| 4 | 382 | 0.73 | 0.84 | 58 | empty |
| 5 | 378 | 0.73 | 0.84 | 54 | empty |
Interfaces
15 interfaces between chains.
- B–D · 1487 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 1447 Ų buried · 16 hydrogen bonds · protein-protein
- E–L · 1443 Ų buried · 15 hydrogen bonds · protein-protein
- C–I · 1437 Ų buried · 13 hydrogen bonds · protein-protein
- J–K · 1431 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (nonstandard).
Compared structures
- 7L4B · Dihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate bound in the active site… · the same entry in another collection · chain L against L, 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 7L4B · PDBe 7L4B · UniProt Q9PPB4
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