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Structure of the yeast clamp loader (replication factor C rfc) bound to the sliding clamp (proliferating cell nuclear antigen PCNA) in an autoinhibited conformation

Analyse Structure of the yeast clamp loader (replication factor C rfc) bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7THJ
Type: protein
Length: 2,554 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Replication factor C subunit 1; Replication factor C subunit 4; Replication factor C…
UniProt: P38630, P40339, P38629, P40348, P38251, P15873
Ligands: AGS, ADP, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 7 distinct chains · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Replication factor C subunit 1	protein	482	55% helix, 6% strand	P38630
B	Replication factor C subunit 4	protein	315	57% helix, 10% strand	P40339
C	Replication factor C subunit 3	protein	322	60% helix, 9% strand	P38629
D	Replication factor C subunit 2	protein	328	52% helix, 8% strand	P40348
E	Replication factor C subunit 5	protein	338	49% helix, 13% strand	P38251
F, H	Proliferating cell nuclear antigen	protein	256	15% helix, 45% strand	P15873
G	Proliferating cell nuclear antigen	protein	257	18% helix, 46% strand	P15873

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D, E
ADP · Adenosine-5'-diphosphate · ligand · chains A, E
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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	1179	0.87	0.88	127	AGS, MG
2	1003	0.84	0.85	86	ADP
3	1018	0.83	0.84	102	empty
4	829	0.81	0.83	81	AGS, MG
5	80	0.78	0.98	20	empty

Interfaces

14 interfaces between chains.

A–E · 2946 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2852 Å² buried · 33 hydrogen bonds · protein-protein
D–E · 1996 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1845 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1156 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7THJ · Structure of the yeast clamp loader (Replication Factor C RFC) bound to the sliding clamp… · the same entry in another collection · chain G against G, TM-score 1.00
P40339 · AlphaFold monomer V2.0 prediction for replication factor C subunit 4 (P40339) · a predicted model of the same protein · chain B against A, TM-score 0.98
P38629 · AlphaFold monomer V2.0 prediction for replication factor C subunit 3 (P38629) · a predicted model of the same protein · chain C against A, TM-score 0.97
P38251 · AlphaFold monomer V2.0 prediction for replication factor C subunit 5 (P38251) · a predicted model of the same protein · chain E against A, TM-score 0.97
P40348 · AlphaFold monomer V2.0 prediction for replication factor C subunit 2 (P40348) · a predicted model of the same protein · chain D against A, TM-score 0.90

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 P38630
Every structure of UniProt P40339
Every structure of UniProt P38629
Every structure of UniProt P40348
Every structure of UniProt P38251
Every structure of UniProt P15873
Elsewhere: RCSB PDB 7THJ · PDBe 7THJ · UniProt P38630 · UniProt P40339 · UniProt P38629 · UniProt P40348 · UniProt P38251 · UniProt P15873

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