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The crystal structure of human 6 pyruvoyl tetrahydrobiopterin synthase
Analyse The crystal structure of human 6 pyruvoyl tetrahydrobiopterin synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I2B
- Type
- protein
- Length
- 1,651 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-pyruvoyl tetrahydrobiopterin synthase
- EC
- 4.2.3.12
- UniProt
- Q03393
- Ligands
- NI, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, B, F, I, K, L | 6-pyruvoyl tetrahydrobiopterin synthase (EC 4.2.3.12) | protein | 138 | 36% helix, 32% strand | Q03393 |
| C, H, J | 6-pyruvoyl tetrahydrobiopterin synthase (EC 4.2.3.12) | protein | 137 | 36% helix, 32% strand | Q03393 |
| G | 6-pyruvoyl tetrahydrobiopterin synthase (EC 4.2.3.12) | protein | 136 | 38% helix, 32% strand | Q03393 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 12 copies · chains A, D, E, B, C, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 2 copies · chains A, E, J, K
- EDO · 1,2-ethanediol · additive · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.79 | 0.83 | 47 | PEG |
| 2 | 539 | 0.78 | 0.85 | 48 | empty |
| 3 | 453 | 0.78 | 0.86 | 47 | empty |
| 4 | 672 | 0.77 | 0.83 | 102 | empty |
| 5 | 607 | 0.77 | 0.83 | 49 | empty |
Interfaces
22 interfaces between chains.
- A–D · 850 Ų buried · 12 hydrogen bonds · protein-protein
- A–G · 837 Ų buried · 22 hydrogen bonds · protein-protein
- D–I · 836 Ų buried · 21 hydrogen bonds · protein-protein
- E–H · 825 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 811 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3I2B · The crystal structure of human 6 Pyruvoyl Tetrahydrobiopterin Synthase · the same entry in another collection · chain L against L, 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 Q03393
- Elsewhere: RCSB PDB 3I2B · PDBe 3I2B · UniProt Q03393
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