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Crystal structure of dihydrodipicolinate synthase dapa-2 (BA3935) from bacillus anthracis at 1.94A resolution.
Analyse Crystal structure of dihydrodipicolinate synthase dapa-2 (BA3935) from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XKY
- Type
- protein
- Length
- 1,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q81WN7
- Ligands
- K
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 292 | 49% helix, 13% strand | Q81WN7 |
Ligands and binding sites
- K · Potassium ion · metal · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.77 | 0.80 | 125 | empty |
| 2 | 594 | 0.75 | 0.82 | 75 | empty |
| 3 | 403 | 0.64 | 0.78 | 64 | empty |
| 4 | 135 | 0.42 | 0.75 | 29 | K |
| 5 | 116 | 0.41 | 0.76 | 27 | K |
Interfaces
4 interfaces between chains.
- C–D · 1408 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1407 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 942 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 926 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1XKY · Crystal Structure of Dihydrodipicolinate Synthase DapA-2 (BA3935) from Bacillus Anthracis… · 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 Q81WN7
- Elsewhere: RCSB PDB 1XKY · PDBe 1XKY · UniProt Q81WN7
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