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The crystal structure of a putative aminotransferase from corynebacterium diphtheriae
Analyse The crystal structure of a putative aminotransferase from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D6K
- Type
- protein
- Length
- 1,639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aminotransferase
- UniProt
- Q6NJY4
- Ligands
- SO4, CL
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative aminotransferase | protein | 405 | 44% helix, 15% strand | Q6NJY4 |
| B | Putative aminotransferase | protein | 409 | 44% helix, 15% strand | Q6NJY4 |
| C | Putative aminotransferase | protein | 413 | 44% helix, 15% strand | Q6NJY4 |
| D | Putative aminotransferase | protein | 412 | 44% helix, 14% strand | Q6NJY4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.81 | 0.83 | 107 | CL |
| 2 | 136 | 0.79 | 0.97 | 34 | empty |
| 3 | 106 | 0.79 | 0.99 | 22 | empty |
| 4 | 108 | 0.79 | 0.98 | 23 | empty |
| 5 | 139 | 0.79 | 0.96 | 34 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2371 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2355 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 467 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 440 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 183 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 3D6K · The crystal structure of a putative aminotransferase from Corynebacterium diphtheriae · 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 Q6NJY4
- Elsewhere: RCSB PDB 3D6K · PDBe 3D6K · UniProt Q6NJY4
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