Research workbench

Structure of RAD14 in complex with cisplatin containing DNA

Analyse Structure of RAD14 in complex with cisplatin containing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5A39
Type: protein + DNA
Length: 311 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein RAD14; DNA; 5'-D(*DTP*GP*AP*TP*GP*AP*CP*CP*GP*TP*AP*GP*AP)-3'…
UniProt: P28519
Ligands: CPT, ZN
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 5 distinct chains · 49% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair protein RAD14	protein	114	49% helix, 10% strand	P28519
B	DNA repair protein RAD14	protein	115	49% helix, 10% strand	P28519
C, D	DNA	dna	15	—	—
E, F	5'-D(DTPGPAPTPGPAPCPCPGPTPAPGP*AP)-3'	dna	13	—	—
G, H	5'-D(DGPAPTPGPAPCPCPGPTPAPGPAP*GP)-3'	dna	13	—	—

Ligands and binding sites

CPT · Cisplatin · ligand · 4 copies · chains C, E, F, G, H, D
ZN · Zinc ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	396	0.63	0.78	59	CPT
2	475	0.60	0.74	42	empty
3	51	0.29	0.75	12	empty

Interfaces

22 interfaces between chains.

D–E · 1514 Å² buried · 585 hydrogen bonds · nucleic-nucleic
F–H · 1509 Å² buried · 532 hydrogen bonds · nucleic-nucleic
C–F · 1504 Å² buried · 573 hydrogen bonds · nucleic-nucleic
D–G · 1487 Å² buried · 567 hydrogen bonds · nucleic-nucleic
C–H · 1478 Å² buried · 548 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 10 covalent (covalent ligand).

Compared structures

5A39 · Structure of Rad14 in complex with cisplatin containing DNA · the same entry in another collection · chain H against H, TM-score 1.00
P28519 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD14 (P28519) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P28519
Elsewhere: RCSB PDB 5A39 · PDBe 5A39 · UniProt P28519

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.