Research workbench
GRB7-SH2 domain in complex with bicyclic peptide B8
Analyse GRB7-SH2 domain in complex with bicyclic peptide B8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MP3
- Type
- protein
- Length
- 420 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth factor receptor-bound protein 7; Bicyclic peptide B8
- UniProt
- Q14451
- Ligands
- 48V
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Growth factor receptor-bound protein 7 | protein | 102 | 20% helix, 33% strand | Q14451 |
| B | Growth factor receptor-bound protein 7 | protein | 97 | 18% helix, 35% strand | Q14451 |
| D | Growth factor receptor-bound protein 7 | protein | 99 | 17% helix, 34% strand | Q14451 |
| L, N | Bicyclic peptide B8 | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- 48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · 2 copies · chains C, L, A, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.56 | 0.75 | 33 | empty |
| 2 | 54 | 0.31 | 0.76 | 21 | empty |
Interfaces
8 interfaces between chains.
- C–N · 478 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 476 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 471 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 464 Ų buried · 4 hydrogen bonds · protein-protein
- C–L · 212 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 isopeptide (covalent ligand, isopeptide).
Compared structures
- 7MP3 · Grb7-SH2 domain in complex with bicyclic peptide B8 · the same entry in another collection · chain N against N, TM-score 1.00
- Q14451 · AlphaFold monomer V2.0 prediction for growth factor receptor-bound protein 7 (Q14451) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q14451
- Elsewhere: RCSB PDB 7MP3 · PDBe 7MP3 · UniProt Q14451
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