MolNFT v1 · #68204 · protein

Structure of the eukaryotic replicative cmg helicase and pumpjack motion

3JC5 · DNA replication licensing factor MCM2: “Structure of the eukaryotic replicative cmg helicase and pumpjack motion”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #68204 on GenesisL1: 3D structure, binding sites…

PDB: 3JC5
Type: protein
Length: 5,039 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
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	584	38% helix, 12% strand	P29469
3	DNA replication licensing factor MCM3 (EC 3.6.4.12)	protein	588	33% helix, 14% strand	P24279
4	DNA replication licensing factor MCM4 (EC 3.6.4.12)	protein	569	33% helix, 13% strand	P30665
5	Minichromosome maintenance protein 5 (EC 3.6.4.12)	protein	653	39% helix, 14% strand	P29496
6	DNA replication licensing factor MCM6 (EC 3.6.4.12)	protein	671	35% helix, 12% strand	P53091
7	DNA replication licensing factor MCM7 (EC 3.6.4.12)	protein	652	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

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	1187	0.88	0.89	145	empty
2	921	0.87	0.89	107	empty
3	861	0.86	0.88	106	empty
4	1011	0.84	0.85	129	empty
5	987	0.84	0.85	104	empty

Interfaces

27 interfaces between chains.

3–7 · 3843 Å² buried · 31 hydrogen bonds · protein-protein
2–6 · 3776 Å² buried · 26 hydrogen bonds · protein-protein
4–7 · 3522 Å² buried · 64 hydrogen bonds · protein-protein
3–5 · 3358 Å² buried · 20 hydrogen bonds · protein-protein
2–5 · 2805 Å² buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 isopeptide, 2 disulfide (isopeptide, disulfide).

Compared structures

3JC5 · 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 3JC5 · PDBe 3JC5 · 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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