MolNFT v1 · #34076 · protein
Crystal structure of the endophilin bar domain mutant
2D4C · SH3-containing GRB2-like protein 2: “Crystal structure of the endophilin bar domain mutant”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.75). MolNFT v1 #34076 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2D4C
- Type
- protein
- Length
- 898 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SH3-containing GRB2-like protein 2
- EC
- 2.3.1.-
- UniProt
- Q99962
- Ligands
- CA
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 89% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SH3-containing GRB2-like protein 2 (EC 2.3.1.-) | protein | 224 | 89% helix, 0% strand | Q99962 |
| B | SH3-containing GRB2-like protein 2 (EC 2.3.1.-) | protein | 231 | 89% helix, 0% strand | Q99962 |
| C | SH3-containing GRB2-like protein 2 (EC 2.3.1.-) | protein | 226 | 88% helix, 0% strand | Q99962 |
| D | SH3-containing GRB2-like protein 2 (EC 2.3.1.-) | protein | 217 | 90% helix, 0% strand | Q99962 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.75 | 0.89 | 41 | empty |
| 2 | 214 | 0.74 | 0.89 | 38 | empty |
| 3 | 237 | 0.60 | 0.80 | 40 | empty |
| 4 | 94 | 0.52 | 0.83 | 21 | empty |
| 5 | 142 | 0.51 | 0.79 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2721 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2657 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 542 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
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 Q99962
- Elsewhere: RCSB PDB 2D4C · PDBe 2D4C · UniProt Q99962
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