MolNFT v1 · #146591 · protein
Crystal structure of the SH2 domain from ravo (LPG1129) from legionella pneumophila in complex with homo sapiens SHC1 phospho- TYR317 peptide
6DM4: “Crystal structure of the SH2 domain from ravo (LPG1129) from legionella pneumophila in complex with homo…”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.74). MolNFT v1 #146591 on GenesisL1: 3D structure, binding…
- PDB
- 6DM4
- Type
- protein
- Length
- 496 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ravo; SHC1 phospho-TYR317 peptide
- UniProt
- Q5ZWF6
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ravo | protein | 119 | 36% helix, 28% strand | Q5ZWF6 |
| E, H | SHC1 phospho-TYR317 peptide | protein | 7 | 0% helix, 14% strand | — |
| G | SHC1 phospho-TYR317 peptide | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.74 | 0.79 | 62 | SO4 |
| 2 | 178 | 0.44 | 0.74 | 34 | SO4 |
| 3 | 92 | 0.43 | 0.79 | 21 | empty |
| 4 | 64 | 0.39 | 0.80 | 18 | empty |
| 5 | 114 | 0.37 | 0.74 | 25 | empty |
Interfaces
8 interfaces between chains.
- C–D · 838 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 828 Ų buried · 6 hydrogen bonds · protein-protein
- D–H · 539 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 528 Ų buried · 16 hydrogen bonds · protein-protein
- C–G · 455 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 6DM4 · Crystal structure of the SH2 domain from RavO (Lpg1129) from Legionella pneumophila in… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5ZWF6
- Elsewhere: RCSB PDB 6DM4 · PDBe 6DM4 · UniProt Q5ZWF6
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