Research workbench
Crystal structure of RV3772 in complex with its substrate
Analyse Crystal structure of RV3772 in complex with its substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R2N
- Type
- protein
- Length
- 1,412 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phenylalanine aminotransferase
- EC
- 2.6.1.-
- UniProt
- I6Y4H4
- Ligands
- PLP, PHE
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative phenylalanine aminotransferase (EC 2.6.1.-) | protein | 353 | 42% helix, 16% strand | I6Y4H4 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, C, B, D
- PHE · Phenylalanine · ligand · 4 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.81 | 0.83 | 80 | EPE |
| 2 | 119 | 0.77 | 0.96 | 27 | PLP, PHE |
| 3 | 819 | 0.73 | 0.78 | 79 | PLP, PHE |
| 4 | 817 | 0.72 | 0.77 | 84 | PLP, PHE |
| 5 | 356 | 0.72 | 0.84 | 59 | PLP, PHE |
Interfaces
3 interfaces between chains.
- A–C · 3337 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 3331 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 597 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4R2N · Crystal structure of Rv3772 in complex with its substrate · the same entry in another collection · chain C against C, 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 I6Y4H4
- Elsewhere: RCSB PDB 4R2N · PDBe 4R2N · UniProt I6Y4H4
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