Research workbench

Cryo-EM structure of the CDT1-MCM2-7 complex in amppnp state

Analyse Cryo-EM structure of the CDT1-MCM2-7 complex in amppnp state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XF8
Type: protein
Length: 4,283 residues
Chains: 7
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, P47112
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 7 distinct chains · 38% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	DNA replication licensing factor MCM2 (EC 3.6.4.12)	protein	591	41% helix, 13% strand	P29469
3	DNA replication licensing factor MCM3 (EC 3.6.4.12)	protein	601	37% helix, 15% strand	P24279
4	DNA replication licensing factor MCM4 (EC 3.6.4.12)	protein	716	38% helix, 11% strand	P30665
5	Minichromosome maintenance protein 5 (EC 3.6.4.12)	protein	632	42% helix, 17% strand	P29496
6	DNA replication licensing factor MCM6 (EC 3.6.4.12)	protein	652	39% helix, 12% strand	P53091
7	DNA replication licensing factor MCM7 (EC 3.6.4.12)	protein	622	34% helix, 16% strand	P38132
C	Cell division cycle protein CDT1	protein	469	39% helix, 13% strand	P47112

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	1120	0.82	0.83	161	empty
2	1014	0.81	0.82	133	empty
3	1176	0.80	0.82	125	empty
4	771	0.79	0.83	126	empty
5	850	0.78	0.82	96	empty

Interfaces

9 interfaces between chains.

3–5 · 1237 Å² buried · 1 hydrogen bond · protein-protein
3–7 · 1158 Å² buried · 9 hydrogen bonds · protein-protein
4–6 · 613 Å² buried · 0 hydrogen bonds · protein-protein
4–7 · 600 Å² buried · 7 hydrogen bonds · protein-protein
2–6 · 563 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5XF8 · Cryo-EM structure of the Cdt1-MCM2-7 complex in AMPPNP state · the same entry in another collection · chain C against C, TM-score 1.00
P38132 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM7 (P38132) · a predicted model of the same protein · chain 7 against A, TM-score 0.75
P29496 · AlphaFold monomer V2.0 prediction for minichromosome maintenance protein 5 (P29496) · a predicted model of the same protein · chain 5 against A, TM-score 0.71
P24279 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM3 (P24279) · a predicted model of the same protein · chain 3 against A, TM-score 0.71
P53091 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM6 (P53091) · a predicted model of the same protein · chain 6 against A, TM-score 0.70
P47112 · AlphaFold monomer V2.0 prediction for cell division cycle protein CDT1 (P47112) · a predicted model of the same protein · chain C against A, TM-score 0.67

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 P47112
Elsewhere: RCSB PDB 5XF8 · PDBe 5XF8 · UniProt P29469 · UniProt P24279 · UniProt P30665 · UniProt P29496 · UniProt P53091 · UniProt P38132 · UniProt P47112

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