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Crystal structure of dipicolinate synthase subunit a (NP_243269.1) from bacillus halodurans at 2.10 a resolution
Analyse Crystal structure of dipicolinate synthase subunit a (NP_243269.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D4O
- Type
- protein
- Length
- 1,162 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipicolinate synthase subunit a
- UniProt
- Q9KA87
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipicolinate synthase subunit a | protein | 290 | 41% helix, 20% strand | Q9KA87 |
| B | Dipicolinate synthase subunit a | protein | 291 | 41% helix, 20% strand | Q9KA87 |
| C | Dipicolinate synthase subunit a | protein | 291 | 41% helix, 20% strand | Q9KA87 |
| D | Dipicolinate synthase subunit a | protein | 290 | 41% helix, 20% strand | Q9KA87 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, D, C
- TAR · D(-)-tartaric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.80 | 0.82 | 63 | EDO |
| 2 | 375 | 0.65 | 0.79 | 41 | EDO |
| 3 | 394 | 0.64 | 0.78 | 53 | empty |
| 4 | 352 | 0.63 | 0.79 | 43 | TAR |
| 5 | 382 | 0.61 | 0.77 | 48 | EDO |
Interfaces
6 interfaces between chains.
- A–C · 1017 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1006 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 830 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 819 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 124 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 3D4O · Crystal structure of dipicolinate synthase subunit A (NP_243269.1) from BACILLUS… · 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 Q9KA87
- Elsewhere: RCSB PDB 3D4O · PDBe 3D4O · UniProt Q9KA87
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