MolNFT v1 · #74773 · protein
Crystal structure of a plp-dependent aminotransferase (ZP_03625122.1) from streptococcus suis 89-1591 at 2.07 a resolution
3P6K · Aminotransferase class I and II: “Crystal structure of a plp-dependent aminotransferase (ZP_03625122.1) from streptococcus suis 89-1591 at 2.07…”. X-ray diffraction, 2 ligands (UNL, SO4), 4 pockets (best druggability 0.73). MolNFT…
- PDB
- 3P6K
- Type
- protein
- Length
- 743 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase class I and II
- UniProt
- B9WVA1
- Ligands
- UNL, SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase class I and II | protein | 369 | 47% helix, 16% strand | B9WVA1 |
| B | Aminotransferase class I and II | protein | 374 | 46% helix, 17% strand | B9WVA1 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.73 | 0.82 | 55 | SO4, UNL |
| 2 | 379 | 0.68 | 0.81 | 50 | UNL, SO4 |
| 3 | 169 | 0.62 | 0.84 | 23 | empty |
| 4 | 170 | 0.60 | 0.83 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2872 Ų buried · 64 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (engineered, cofactor).
Compared structures
- 3P6K · Crystal structure of a PLP-dependent aminotransferase (ZP_03625122.1) from Streptococcus… · 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 B9WVA1
- Elsewhere: RCSB PDB 3P6K · PDBe 3P6K · UniProt B9WVA1
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