MolNFT v1 · #188676 · protein + DNA

Cryo-EM structure of human cst bound to DNA polymerase alpha-primase in a recruitment state

7U5C · DNA primase small subunit: “Cryo-EM structure of human cst bound to DNA polymerase alpha-primase in a recruitment state”. Electron microscopy, 2 ligands (SF4, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #188676 on GenesisL1…

PDB: 7U5C
Type: protein + DNA
Length: 3,744 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA primase small subunit; DNA primase large subunit; DNA polymerase alpha catalytic…
EC: 2.7.7.-, 2.7.7.7
UniProt: P49642, P49643, P09884, Q14181, Q2NKJ3, Q9H668, Q86WV5
Ligands: SF4, ZN
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 8 distinct chains · 29% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA primase small subunit (EC 2.7.7.-)	protein	386	42% helix, 11% strand	P49642
B	DNA primase large subunit (EC 2.7.7.-)	protein	434	53% helix, 2% strand	P49643
C	DNA polymerase alpha catalytic subunit (EC 2.7.7.7)	protein	1057	37% helix, 17% strand	P09884
D	DNA polymerase alpha subunit B	protein	444	20% helix, 22% strand	Q14181
E	Cst complex subunit CTC1	protein	1147	15% helix, 25% strand	Q2NKJ3
F	Cst complex subunit STN1	protein	155	25% helix, 29% strand	Q9H668
G	Cst complex subunit TEN1	protein	117	12% helix, 32% strand	Q86WV5
H	Canonical telomeric DNA sequence	dna	4	—	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains B
ZN · Zinc ion · metal · 4 copies · chains A, C, E

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	1008	0.84	0.85	98	empty
2	633	0.82	0.87	70	empty
3	1155	0.81	0.82	115	empty
4	250	0.81	0.93	51	empty
5	563	0.81	0.86	73	empty

Interfaces

12 interfaces between chains.

B–C · 2634 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 2601 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 1840 Å² buried · 23 hydrogen bonds · protein-protein
F–G · 1360 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 740 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

7U5C · Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment… · the same entry in another collection · chain H against H, TM-score 1.00
Q14181 · AlphaFold monomer V2.0 prediction for DNA polymerase alpha subunit B (Q14181) · a predicted model of the same protein · chain D against A, TM-score 0.96
Q2NKJ3 · AlphaFold monomer V2.0 prediction for cst complex subunit CTC1 (Q2NKJ3) · a predicted model of the same protein · chain E against A, TM-score 0.95
P49642 · AlphaFold monomer V2.0 prediction for DNA primase small subunit (P49642) · a predicted model of the same protein · chain A against A, TM-score 0.94
P49643 · AlphaFold monomer V2.0 prediction for DNA primase large subunit (P49643) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 P49642
Every structure of UniProt P49643
Every structure of UniProt P09884
Every structure of UniProt Q14181
Every structure of UniProt Q2NKJ3
Every structure of UniProt Q9H668
Every structure of UniProt Q86WV5
Elsewhere: RCSB PDB 7U5C · PDBe 7U5C · UniProt P49642 · UniProt P49643 · UniProt P09884 · UniProt Q14181 · UniProt Q2NKJ3 · UniProt Q9H668 · UniProt Q86WV5

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