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Structure of the human clamp loader (replication factor C, rfc) bound to the sliding clamp (proliferating cell nuclear antigen, PCNA)

Analyse Structure of the human 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: 6VVO
Type: protein
Length: 2,493 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Replication factor C subunit 1; Replication factor C subunit 2; Replication factor C…
UniProt: P35251, P35250, P40937, P35249, P40938, P12004
Ligands: AGS, ADP, MG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 8 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Replication factor C subunit 1	protein	448	54% helix, 5% strand	P35251
B	Replication factor C subunit 2	protein	316	59% helix, 9% strand	P35250
C	Replication factor C subunit 5	protein	312	54% helix, 9% strand	P40937
D	Replication factor C subunit 4	protein	304	54% helix, 9% strand	P35249
E	Replication factor C subunit 3	protein	346	52% helix, 12% strand	P40938
F	Proliferating cell nuclear antigen	protein	254	15% helix, 42% strand	P12004
G	Proliferating cell nuclear antigen	protein	257	18% helix, 45% strand	P12004
H	Proliferating cell nuclear antigen	protein	256	16% helix, 41% strand	P12004

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
ADP · Adenosine-5'-diphosphate · ligand · chains 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	875	0.83	0.86	90	MG, AGS
2	1175	0.82	0.83	102	empty
3	560	0.81	0.87	63	empty
4	302	0.80	0.91	43	ADP
5	212	0.80	0.94	36	MG, AGS

Interfaces

15 interfaces between chains.

A–E · 3099 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2497 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 2114 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 2034 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1899 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6VVO · Structure of the human clamp loader (Replication Factor C, RFC) bound to the sliding… · the same entry in another collection · chain H against H, TM-score 1.00
P40938 · AlphaFold monomer V2.0 prediction for replication factor C subunit 3 (P40938) · a predicted model of the same protein · chain E against A, TM-score 0.98
P35250 · AlphaFold monomer V2.0 prediction for replication factor C subunit 2 (P35250) · a predicted model of the same protein · chain B against A, TM-score 0.96
P40937 · AlphaFold monomer V2.0 prediction for replication factor C subunit 5 (P40937) · a predicted model of the same protein · chain C against A, TM-score 0.95
P35249 · AlphaFold monomer V2.0 prediction for replication factor C subunit 4 (P35249) · a predicted model of the same protein · chain D 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 P35251
Every structure of UniProt P35250
Every structure of UniProt P40937
Every structure of UniProt P35249
Every structure of UniProt P40938
Every structure of UniProt P12004
Elsewhere: RCSB PDB 6VVO · PDBe 6VVO · UniProt P35251 · UniProt P35250 · UniProt P40937 · UniProt P35249 · UniProt P40938 · UniProt P12004

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