Research workbench
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 v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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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