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Crystal structure of RV3772 encoded aminotransferase
Analyse Crystal structure of RV3772 encoded aminotransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R5Z
- 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
- PMP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative phenylalanine aminotransferase (EC 2.6.1.-) | protein | 353 | 43% helix, 16% strand | I6Y4H4 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 20 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 4 copies · chains A, B, C, 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
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.85 | 0.87 | 87 | empty |
| 2 | 78 | 0.76 | 0.99 | 25 | SIN, PMP |
| 3 | 77 | 0.73 | 0.97 | 24 | SIN, PMP |
| 4 | 98 | 0.73 | 0.95 | 31 | SIN, PMP |
| 5 | 89 | 0.70 | 0.94 | 33 | SIN, PMP |
Interfaces
6 interfaces between chains.
- A–B · 3289 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 3276 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 617 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 316 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 106 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4R5Z · Crystal structure of Rv3772 encoded aminotransferase · 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 I6Y4H4
- Elsewhere: RCSB PDB 4R5Z · PDBe 4R5Z · UniProt I6Y4H4
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