MolNFT v1 · #38046 · protein
Crystal structure of the SGPB:P14'-ALA32 OMTKY3-DEL(1-5) complex
2GKV · Streptogrisin B: “Crystal structure of the SGPB:P14'-ALA32 OMTKY3-DEL(1-5) complex”. X-ray diffraction, 3 pockets (best druggability 0.53). MolNFT v1 #38046 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GKV
- Type
- protein
- Length
- 287 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptogrisin B; Ovomucoid
- EC
- 3.4.21.81
- UniProt
- P00777, P68390
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Streptogrisin B (EC 3.4.21.81) | protein | 185 | 6% helix, 53% strand | P00777 |
| A, B | Ovomucoid | protein | 51 | 20% helix, 24% strand | P68390 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.53 | 0.77 | 34 | empty |
| 2 | 69 | 0.45 | 0.82 | 20 | empty |
| 3 | 53 | 0.30 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- E–A · 641 Ų buried · 14 hydrogen bonds · protein-protein
- E–B · 625 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2GKV · Crystal structure of the SGPB:P14'-Ala32 OMTKY3-del(1-5) complex · 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 A against A, TM-score 0.93
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 2GKV · PDBe 2GKV · UniProt P00777 · UniProt P68390
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