Research workbench
E.COLI qued, semet protein, 2A resolution
Analyse E.COLI qued, semet protein, 2A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NTN
- Type
- protein
- Length
- 710 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
- P65870
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50) | protein | 118 | 28% helix, 34% strand | P65870 |
| B, D | 6-carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50) | protein | 119 | 28% helix, 34% strand | P65870 |
| C | 6-carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50) | protein | 117 | 28% helix, 34% strand | P65870 |
| E | 6-carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50) | protein | 119 | 28% helix, 34% strand | P65870 |
| F | 6-carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50) | protein | 118 | 28% helix, 31% strand | P65870 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.77 | 0.79 | 112 | empty |
| 2 | 646 | 0.74 | 0.81 | 76 | ZN |
| 3 | 484 | 0.72 | 0.81 | 62 | ZN |
| 4 | 394 | 0.65 | 0.79 | 33 | empty |
| 5 | 120 | 0.44 | 0.77 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–B · 780 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 758 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 756 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 751 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 743 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
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 P65870
- Elsewhere: RCSB PDB 4NTN · PDBe 4NTN · UniProt P65870
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