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Crystal structure of synechocystis arogenate dehydrogenase
Analyse Crystal structure of synechocystis arogenate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F1K
- Type
- protein
- Length
- 1,115 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prephenate dehydrogenase
- EC
- 1.3.1.43
- UniProt
- P73906
- Ligands
- NAP
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Prephenate dehydrogenase (EC 1.3.1.43) | protein | 279 | 59% helix, 13% strand | P73906 |
| C | Prephenate dehydrogenase (EC 1.3.1.43) | protein | 278 | 59% helix, 13% strand | P73906 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.81 | 0.83 | 113 | NAP, TRS |
| 2 | 977 | 0.80 | 0.81 | 90 | NAP |
| 3 | 648 | 0.77 | 0.82 | 64 | NAP |
| 4 | 1153 | 0.75 | 0.78 | 96 | NAP |
| 5 | 170 | 0.54 | 0.80 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4296 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 4291 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 669 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 606 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 603 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 2F1K · Crystal structure of Synechocystis arogenate dehydrogenase · 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 P73906
- Elsewhere: RCSB PDB 2F1K · PDBe 2F1K · UniProt P73906
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