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
- 2NU3
- Type
- protein
- Length
- 236 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptogrisin B, proteinase B; Ovomucoid
- EC
- 3.4.21.81
- UniProt
- P00777, P68390
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 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 | 140 | 0.44 | 0.76 | 26 | empty |
| 2 | 120 | 0.37 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- E–I · 652 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2NU3 · 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 2NU3 · PDBe 2NU3 · UniProt P00777 · UniProt P68390
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