Research workbench
Agrobacterium tumefaciens dhdps with pyruvate
Analyse Agrobacterium tumefaciens dhdps with pyruvate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I7V
- Type
- protein
- Length
- 1,175 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- F0L8Z6
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 294 | 51% helix, 13% strand | F0L8Z6 |
| B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 293 | 51% helix, 13% strand | F0L8Z6 |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.75 | 0.86 | 57 | empty |
| 2 | 315 | 0.73 | 0.86 | 53 | empty |
| 3 | 312 | 0.62 | 0.79 | 43 | empty |
| 4 | 305 | 0.62 | 0.79 | 40 | empty |
| 5 | 299 | 0.61 | 0.79 | 43 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1484 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1460 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 996 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 982 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 4I7V · Agrobacterium tumefaciens DHDPS with pyruvate · the same entry in another collection · chain C against C, 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 F0L8Z6
- Elsewhere: RCSB PDB 4I7V · PDBe 4I7V · UniProt F0L8Z6
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