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Crystal structure of a 6-pyruvoyltetrahydropterin synthase homologue from esherichia COLI complexed sepiapterin
Analyse Crystal structure of a 6-pyruvoyltetrahydropterin synthase homologue from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QNA
- Type
- protein
- Length
- 708 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-carboxy-5,6,7,8-tetrahydropterin synthase
- EC
- 4.1.2.50
- UniProt
- C6EJA7
- Ligands
- BIO, ZN
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 6-carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50) | protein | 118 | 28% helix, 35% strand | C6EJA7 |
Ligands and binding sites
- BIO · Biopterin · ligand · 6 copies · chains A, B, D, C, F, E
- ZN · Zinc ion · metal · 6 copies · chains A, D, B, F, C, E
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 | 1010 | 0.81 | 0.82 | 120 | BIO, ZN |
| 2 | 213 | 0.67 | 0.85 | 31 | BIO |
| 3 | 310 | 0.66 | 0.81 | 34 | empty |
| 4 | 157 | 0.64 | 0.86 | 30 | BIO, ZN |
| 5 | 143 | 0.63 | 0.86 | 28 | BIO |
Interfaces
9 interfaces between chains.
- B–C · 770 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 767 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 766 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 766 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 756 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3QNA · Crystal structure of a 6-pyruvoyltetrahydropterin synthase homologue from Esherichia coli… · 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 C6EJA7
- Elsewhere: RCSB PDB 3QNA · PDBe 3QNA · UniProt C6EJA7
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