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Crystal structure of prephenate dehydratase from brucella melitensis biovar abortus 2308 in complex with phenylalanine
Analyse Crystal structure of prephenate dehydratase from brucella melitensis biovar… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VH5
- Type
- protein
- Length
- 1,122 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Brucella abortus (strain 2308)
- Molecule
- Prephenate dehydratase:Amino acid-binding ACT
- EC
- 4.2.1.51
- UniProt
- Q2YPM5
- Ligands
- PHE
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.4 · 4 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prephenate dehydratase:Amino acid-binding ACT (EC 4.2.1.51) | protein | 281 | 29% helix, 33% strand | Q2YPM5 |
| B | Prephenate dehydratase:Amino acid-binding ACT (EC 4.2.1.51) | protein | 280 | 31% helix, 34% strand | Q2YPM5 |
| C | Prephenate dehydratase:Amino acid-binding ACT (EC 4.2.1.51) | protein | 279 | 29% helix, 35% strand | Q2YPM5 |
| D | Prephenate dehydratase:Amino acid-binding ACT (EC 4.2.1.51) | protein | 282 | 29% helix, 33% strand | Q2YPM5 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 4 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.87 | 0.88 | 116 | empty |
| 2 | 816 | 0.86 | 0.88 | 86 | empty |
| 3 | 308 | 0.76 | 0.88 | 31 | empty |
| 4 | 66 | 0.74 | 0.98 | 22 | EDO, PHE |
| 5 | 70 | 0.74 | 0.98 | 22 | EDO, PHE |
Interfaces
3 interfaces between chains.
- A–C · 1705 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1618 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 329 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6VH5 · Crystal structure of prephenate dehydratase from brucella melitensis biovar abortus 2308… · 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 Q2YPM5
- Elsewhere: RCSB PDB 6VH5 · PDBe 6VH5 · UniProt Q2YPM5
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