Research workbench

Structure of the eukaryotic replicative cmg helicase and pumpjack motion

Analyse Structure of the eukaryotic replicative cmg helicase and pumpjack motion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JC7
Type: protein
Length: 5,075 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA replication licensing factor MCM2; DNA replication licensing factor MCM3; DNA…
EC: 3.6.4.12
UniProt: P29469, P24279, P30665, P29496, P53091, P38132, Q08032, Q03406, P40359, Q12488, Q12146
Ligands: ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 11 distinct chains · 38% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	DNA replication licensing factor MCM2 (EC 3.6.4.12)	protein	576	38% helix, 12% strand	P29469
3	DNA replication licensing factor MCM3 (EC 3.6.4.12)	protein	577	35% helix, 14% strand	P24279
4	DNA replication licensing factor MCM4 (EC 3.6.4.12)	protein	621	31% helix, 13% strand	P30665
5	Minichromosome maintenance protein 5 (EC 3.6.4.12)	protein	654	38% helix, 14% strand	P29496
6	DNA replication licensing factor MCM6 (EC 3.6.4.12)	protein	668	36% helix, 12% strand	P53091
7	DNA replication licensing factor MCM7 (EC 3.6.4.12)	protein	657	32% helix, 13% strand	P38132
c	Cell division control protein 45	protein	553	45% helix, 9% strand	Q08032
D	DNA replication complex gins protein SLD5	protein	221	50% helix, 3% strand	Q03406
B	DNA replication complex gins protein PSF2	protein	181	49% helix, 9% strand	P40359
A	DNA replication complex gins protein PSF1	protein	208	53% helix, 5% strand	Q12488
C	DNA replication complex gins protein PSF3	protein	159	47% helix, 8% strand	Q12146

Ligands and binding sites

ZN · Zinc ion · metal · chains 7

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1046	0.88	0.89	127	empty
2	1176	0.88	0.89	129	empty
3	825	0.87	0.90	109	empty
4	1125	0.86	0.87	126	empty
5	1119	0.84	0.85	117	empty

Interfaces

26 interfaces between chains.

3–7 · 4249 Å² buried · 39 hydrogen bonds · protein-protein
3–5 · 3986 Å² buried · 52 hydrogen bonds · protein-protein
4–7 · 3317 Å² buried · 35 hydrogen bonds · protein-protein
2–6 · 2758 Å² buried · 21 hydrogen bonds · protein-protein
4–6 · 2647 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3JC7 · Structure of the eukaryotic replicative CMG helicase and pumpjack motion · the same entry in another collection · chain C against C, TM-score 1.00
Q08032 · AlphaFold monomer V2.0 prediction for cell division control protein 45 (Q08032) · a predicted model of the same protein · chain c against A, TM-score 0.97

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 P29469
Every structure of UniProt P24279
Every structure of UniProt P30665
Every structure of UniProt P29496
Every structure of UniProt P53091
Every structure of UniProt P38132
Every structure of UniProt Q08032
Every structure of UniProt Q03406
Every structure of UniProt P40359
Every structure of UniProt Q12488
Every structure of UniProt Q12146
Elsewhere: RCSB PDB 3JC7 · PDBe 3JC7 · UniProt P29469 · UniProt P24279 · UniProt P30665 · UniProt P29496 · UniProt P53091 · UniProt P38132 · UniProt Q08032 · UniProt Q03406 · UniProt P40359 · UniProt Q12488 · UniProt Q12146

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