Research workbench
Crystal structure of RSU1/PINCH1_LIM45C complex
Analyse Crystal structure of RSU1/PINCH1_LIM45C complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D2T
- Type
- protein
- Length
- 753 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS suppressor protein 1; Lim and senescent cell antigen-like-containing domain protein 1
- UniProt
- Q15404, P48059
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RAS suppressor protein 1 | protein | 247 | 31% helix, 11% strand | Q15404 |
| B | Lim and senescent cell antigen-like-containing domain protein 1 | protein | 130 | 17% helix, 29% strand | P48059 |
| D | Lim and senescent cell antigen-like-containing domain protein 1 | protein | 129 | 19% helix, 29% strand | P48059 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains B, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C
- PGE · Triethylene glycol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.78 | 0.97 | 20 | empty |
| 2 | 186 | 0.72 | 0.89 | 29 | empty |
| 3 | 472 | 0.69 | 0.80 | 41 | empty |
| 4 | 447 | 0.67 | 0.79 | 39 | empty |
| 5 | 134 | 0.45 | 0.77 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1235 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1167 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 758 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 495 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7D2T · Crystal structure of Rsu1/PINCH1_LIM45C complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q15404 · AlphaFold monomer V2.0 prediction for RAS suppressor protein 1 (Q15404) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P48059 · AlphaFold monomer V2.0 prediction for lim and senescent cell antigen- like-containing… · a predicted model of the same protein · chain D against A, TM-score 0.78
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 Q15404
- Every structure of UniProt P48059
- Elsewhere: RCSB PDB 7D2T · PDBe 7D2T · UniProt Q15404 · UniProt P48059
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