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Crystal structure of complex between the domain-swapped dimeric GRB2 SH2 domain and shc-derived ligand, ac-nh-ptyr-val-asn-NH2
Analyse Crystal structure of complex between the domain-swapped dimeric GRB2 SH2 domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H5K
- Type
- protein
- Length
- 195 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth factor receptor-bound protein 2; Shc-derived ligand
- UniProt
- P62993
- Ligands
- ACE, NH2
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Growth factor receptor-bound protein 2 | protein | 96 | 21% helix, 30% strand | P62993 |
| C | Shc-derived ligand | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, C
- NH2 · Amino group · ion · chains A, C
- CAC · Cacodylate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.50 | 0.82 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2545 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 380 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, phosphorylation).
Compared structures
- 2H5K · Crystal Structure of Complex Between the Domain-Swapped Dimeric Grb2 SH2 Domain and… · the same entry in another collection · chain A against A, TM-score 1.00
- P62993 · AlphaFold monomer V2.0 prediction for growth factor receptor-bound protein 2 (P62993) · a predicted model of the same protein · chain A against A, TM-score 0.66
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 P62993
- Elsewhere: RCSB PDB 2H5K · PDBe 2H5K · UniProt P62993
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