Research workbench
Crystal structure of engineered protein at the resolution 1.98A, northeast structural genomics consortium target OR128
Analyse Crystal structure of engineered protein at the resolution 1.98A, northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TP4
- Type
- protein
- Length
- 911 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Computational design of enzyme
- Ligands
- MG
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Computational design of enzyme | protein | 454 | 30% helix, 26% strand | — |
| B | Computational design of enzyme | protein | 457 | 31% helix, 26% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- ACY · Acetic acid · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.78 | 0.80 | 100 | PEG |
| 2 | 146 | 0.59 | 0.83 | 22 | empty |
| 3 | 180 | 0.57 | 0.81 | 37 | empty |
| 4 | 158 | 0.51 | 0.79 | 23 | empty |
| 5 | 71 | 0.43 | 0.81 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 839 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3TP4 · Crystal Structure of engineered protein at the resolution 1.98A, Northeast Structural… · 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
- Elsewhere: RCSB PDB 3TP4 · PDBe 3TP4
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