Research workbench
Accommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I
Analyse Accommodation of positively-charged residues in a hydrophobic specificity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NU4
- Type
- protein
- Length
- 236 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.75
- Source
- Meleagris gallopavo; Streptomyces griseus
- Molecule
- Streptogrisin B, Proteinase B; Ovomucoid
- EC
- 3.4.21.81
- UniProt
- P00777, P68390
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · resolution 1.75 · 2 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Streptogrisin B, Proteinase B (EC 3.4.21.81) | protein | 185 | 6% helix, 53% strand | P00777 |
| I | Ovomucoid | protein | 51 | 20% helix, 24% strand | P68390 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.39 | 0.76 | 17 | empty |
| 2 | 104 | 0.35 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- E–I · 630 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2NU4 · Accommodation of positively-charged residues in a hydrophobic specificity pocket: crystal… · the same entry in another collection · chain E against E, TM-score 1.00
- P00777 · AlphaFold monomer V2.0 prediction for streptogrisin-B (P00777) · a predicted model of the same protein · chain E against A, TM-score 0.99
- P68390 · AlphaFold monomer V2.0 prediction for ovomucoid (P68390) · a predicted model of the same protein · chain I against A, TM-score 0.95
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 P00777
- Every structure of UniProt P68390
- Elsewhere: RCSB PDB 2NU4 · PDBe 2NU4 · UniProt P00777 · UniProt P68390
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.