Research workbench
Crystal structure of dipicolinate synthase, a chain, from bacillus subtilis
Analyse Crystal structure of dipicolinate synthase, a chain, from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RIR
- Type
- protein
- Length
- 2,376 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipicolinate synthase, a chain
- UniProt
- Q04809
- Ligands
- NAP, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, G, H | Dipicolinate synthase, a chain | protein | 297 | 41% helix, 20% strand | Q04809 |
| B | Dipicolinate synthase, a chain | protein | 296 | 42% helix, 20% strand | Q04809 |
| E | Dipicolinate synthase, a chain | protein | 298 | 39% helix, 18% strand | Q04809 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 7 copies · chains A, B, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.80 | 0.82 | 78 | empty |
| 2 | 939 | 0.79 | 0.81 | 66 | empty |
| 3 | 368 | 0.64 | 0.79 | 45 | NAP |
| 4 | 326 | 0.62 | 0.79 | 35 | NAP |
| 5 | 361 | 0.62 | 0.77 | 44 | NAP |
Interfaces
13 interfaces between chains.
- F–H · 992 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 967 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 956 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 929 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 886 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 2RIR · Crystal structure of dipicolinate synthase, A chain, from Bacillus subtilis · the same entry in another collection · chain H against H, TM-score 1.00
- Q04809 · AlphaFold monomer V2.0 prediction for dipicolinate synthase subunit a (Q04809) · a predicted model of the same protein · chain H against A, TM-score 0.98
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 Q04809
- Elsewhere: RCSB PDB 2RIR · PDBe 2RIR · UniProt Q04809
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