Research workbench
Crystal structure of the dipicolinate synthase chain B from bacillus cereus. northeast structural genomics consortium target BCR215.
Analyse Crystal structure of the dipicolinate synthase chain B from bacillus cereus.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MCU
- Type
- protein
- Length
- 1,116 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipicolinate synthase, B chain
- UniProt
- Q819Z6
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipicolinate synthase, B chain | protein | 185 | 39% helix, 21% strand | Q819Z6 |
| B | Dipicolinate synthase, B chain | protein | 187 | 39% helix, 20% strand | Q819Z6 |
| C | Dipicolinate synthase, B chain | protein | 186 | 37% helix, 20% strand | Q819Z6 |
| D | Dipicolinate synthase, B chain | protein | 188 | 37% helix, 20% strand | Q819Z6 |
| E | Dipicolinate synthase, B chain | protein | 183 | 40% helix, 20% strand | Q819Z6 |
| F | Dipicolinate synthase, B chain | protein | 187 | 36% helix, 20% strand | Q819Z6 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 7 copies · chains A, F, C, D, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.84 | 0.92 | 63 | empty |
| 2 | 480 | 0.74 | 0.83 | 72 | empty |
| 3 | 463 | 0.72 | 0.82 | 70 | empty |
| 4 | 481 | 0.72 | 0.82 | 75 | empty |
| 5 | 859 | 0.72 | 0.77 | 85 | PO4 |
Interfaces
12 interfaces between chains.
- C–D · 1039 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1021 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 999 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 645 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 641 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
- 3MCU · Crystal structure of the dipicolinate synthase chain B from Bacillus cereus. Northeast… · 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 Q819Z6
- Elsewhere: RCSB PDB 3MCU · PDBe 3MCU · UniProt Q819Z6
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