Research workbench

Structure of DNA-bound human RAD17-rfc clamp loader and 9-1-1 checkpoint clamp

Analyse Structure of DNA-bound human RAD17-rfc clamp loader and 9-1-1 checkpoint clamp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7Z6H
Type: protein + DNA
Length: 2,545 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell cycle checkpoint control protein RAD9A; Cell cycle checkpoint protein RAD1,CELL…
EC: 3.1.11.2
UniProt: Q99638, O60671, O60921, P35249, P40938, P35250, P40937, O75943
Ligands: AGS
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 10 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cell cycle checkpoint control protein RAD9A (EC 3.1.11.2)	protein	247	17% helix, 36% strand	Q99638
B	Cell cycle checkpoint protein RAD1,CELL cycle checkpoint protein RAD17 (EC 3.1.11.2)	protein	260	12% helix, 40% strand	O60671
C	Checkpoint protein HUS1	protein	273	19% helix, 39% strand	O60921
D	Replication factor C subunit 4	protein	324	56% helix, 7% strand	P35249
E	Replication factor C subunit 3	protein	338	51% helix, 10% strand	P40938
F	Replication factor C subunit 2	protein	315	57% helix, 8% strand	P35250
G	Replication factor C subunit 5	protein	317	56% helix, 7% strand	P40937
K	Cell cycle checkpoint protein RAD1,CELL cycle checkpoint protein RAD17 (EC 3.1.11.2)	protein	439	48% helix, 5% strand	O75943
X	Hairpin DNA	dna	22	—	—
Y	Hairpin DNA	dna	10	—	—

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 5 copies · chains D, E, F, G, K

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	1023	0.85	0.85	95	AGS
2	956	0.82	0.83	97	AGS
3	541	0.81	0.87	65	empty
4	307	0.81	0.92	45	AGS
5	309	0.81	0.91	38	AGS

Interfaces

25 interfaces between chains.

F–K · 2848 Å² buried · 13 hydrogen bonds · protein-protein
E–K · 2487 Å² buried · 9 hydrogen bonds · protein-protein
D–G · 2458 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 2261 Å² buried · 16 hydrogen bonds · protein-protein
F–G · 2258 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent, 1 disulfide (covalent ligand, disulfide).

Compared structures

7Z6H · Structure of DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp · the same entry in another collection · chain Y against Y, TM-score 1.00
O60921 · AlphaFold monomer V2.0 prediction for checkpoint protein HUS1 (O60921) · a predicted model of the same protein · chain C against A, TM-score 0.97
Q99638 · AlphaFold monomer V2.0 prediction for cell cycle checkpoint control protein RAD9A (Q99638) · a predicted model of the same protein · chain A 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 Q99638
Every structure of UniProt O60671
Every structure of UniProt O60921
Every structure of UniProt P35249
Every structure of UniProt P40938
Every structure of UniProt P35250
Every structure of UniProt P40937
Every structure of UniProt O75943
Elsewhere: RCSB PDB 7Z6H · PDBe 7Z6H · UniProt Q99638 · UniProt O60671 · UniProt O60921 · UniProt P35249 · UniProt P40938 · UniProt P35250 · UniProt P40937 · UniProt O75943

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