Research workbench
Crystal structure of the complex of PDZ-rhogef DH/PH domains with GTP- gamma-S activated rhoa
Analyse Crystal structure of the complex of PDZ-rhogef DH/PH domains with GTP- gamma-S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KZ1
- Type
- protein
- Length
- 1,075 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho guanine nucleotide exchange factor 11; Transforming protein rhoa
- UniProt
- O15085, P61586
- Ligands
- GSP, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rho guanine nucleotide exchange factor 11 | protein | 360 | 58% helix, 15% strand | O15085 |
| B | Rho guanine nucleotide exchange factor 11 | protein | 357 | 60% helix, 15% strand | O15085 |
| E, F | Transforming protein rhoa | protein | 179 | 39% helix, 27% strand | P61586 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains E, F
- MG · Magnesium ion · metal · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.79 | 0.81 | 92 | MG, GSP |
| 2 | 1180 | 0.73 | 0.76 | 86 | MG, GSP |
| 3 | 414 | 0.65 | 0.78 | 28 | empty |
| 4 | 426 | 0.63 | 0.77 | 36 | empty |
| 5 | 54 | 0.34 | 0.78 | 10 | empty |
Interfaces
5 interfaces between chains.
- A–B · 796 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 636 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 626 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 508 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 448 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3KZ1 · Crystal Structure of the Complex of PDZ-RhoGEF DH/PH domains with GTP-gamma-S Activated… · the same entry in another collection · chain A against A, TM-score 1.00
- P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain E against A, TM-score 0.99
- O15085 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 11 (O15085) · 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 O15085
- Every structure of UniProt P61586
- Elsewhere: RCSB PDB 3KZ1 · PDBe 3KZ1 · UniProt O15085 · UniProt P61586
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