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Crystal structure of L,L-diaminopimelate aminotransferase (dapl) from verrucomicrobium spinosum
Analyse Crystal structure of L,L-diaminopimelate aminotransferase (dapl) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OXM
- Type
- protein
- Length
- 808 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate aminotransferase
- EC
- 2.6.1.83
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diaminopimelate aminotransferase (EC 2.6.1.83) | protein | 404 | 45% helix, 16% strand | — |
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.78 | 0.82 | 68 | empty |
| 2 | 750 | 0.77 | 0.81 | 64 | empty |
| 3 | 90 | 0.76 | 0.98 | 23 | empty |
| 4 | 72 | 0.74 | 0.99 | 22 | empty |
| 5 | 198 | 0.64 | 0.84 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 3371 Ų buried · 58 hydrogen bonds · protein-protein
Compared structures
- 6OXM · Crystal structure of L,L-diaminopimelate aminotransferase (DapL) from Verrucomicrobium… · 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
- Elsewhere: RCSB PDB 6OXM · PDBe 6OXM
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