MolNFT v1 · #129442 · protein

Crystal structure of the CTF18-1-8 module from CTF18-rfc in complex with a 63 kda fragment of DNA polymerase epsilon

5OKI · DNA polymerase epsilon catalytic subunit a: “Crystal structure of the CTF18-1-8 module from CTF18-rfc in complex with a 63 kda fragment of DNA polymerase…”. X-ray diffraction, 20 pockets (best druggability 0.71). MolNFT v1 #129442…

PDB: 5OKI
Type: protein
Length: 1,967 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase epsilon catalytic subunit a; Sister chromatid cohesion protein DCC1…
EC: 2.7.7.7
UniProt: P21951, P25559, P38877, P49956
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 6 distinct chains · 34% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase epsilon catalytic subunit a (EC 2.7.7.7)	protein	445	40% helix, 23% strand	P21951
B	DNA polymerase epsilon catalytic subunit a (EC 2.7.7.7)	protein	468	36% helix, 22% strand	P21951
C	Sister chromatid cohesion protein DCC1	protein	367	34% helix, 23% strand	P25559
D, H	Chromosome transmission fidelity protein 8	protein	131	11% helix, 55% strand	P38877
E, I	Chromosome transmission fidelity protein 18	protein	26	15% helix, 23% strand	P49956
G	Sister chromatid cohesion protein DCC1	protein	373	33% helix, 23% strand	P25559

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	167	0.71	0.89	29	empty
2	819	0.70	0.76	80	empty
3	125	0.68	0.89	28	empty
4	265	0.63	0.81	29	empty
5	261	0.63	0.81	40	empty

Interfaces

11 interfaces between chains.

G–H · 2783 Å² buried · 46 hydrogen bonds · protein-protein
C–D · 2633 Å² buried · 42 hydrogen bonds · protein-protein
D–E · 1000 Å² buried · 10 hydrogen bonds · protein-protein
H–I · 934 Å² buried · 10 hydrogen bonds · protein-protein
G–I · 862 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5OKI · Crystal structure of the Ctf18-1-8 module from Ctf18-RFC in complex with a 63 kDa… · the same entry in another collection · chain I against I, TM-score 1.00
P21951 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon catalytic subunit a (P21951) · a predicted model of the same protein · chain A against A, TM-score 0.98
P25559 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein DCC1 (P25559) · a predicted model of the same protein · chain G against A, TM-score 0.87

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 P21951
Every structure of UniProt P25559
Every structure of UniProt P38877
Every structure of UniProt P49956
Elsewhere: RCSB PDB 5OKI · PDBe 5OKI · UniProt P21951 · UniProt P25559 · UniProt P38877 · UniProt P49956

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