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Crystal structure of the human sliding clamp at 2.0 ångström resolution

Analyse Crystal structure of the human sliding clamp at 2.0 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RJF
Type: protein
Length: 814 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proliferating cell nuclear antigen; Cyclin-dependent kinase inhibitor 1
UniProt: P12004, P38936
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 6 distinct chains · 17% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proliferating cell nuclear antigen	protein	255	17% helix, 48% strand	P12004
B	Cyclin-dependent kinase inhibitor 1	protein	20	15% helix, 40% strand	P38936
C	Proliferating cell nuclear antigen	protein	253	17% helix, 49% strand	P12004
D	Cyclin-dependent kinase inhibitor 1	protein	19	16% helix, 42% strand	P38936
E	Proliferating cell nuclear antigen	protein	249	16% helix, 48% strand	P12004
F	Cyclin-dependent kinase inhibitor 1	protein	18	17% helix, 33% strand	P38936

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	82	0.78	0.99	24	empty
2	1056	0.73	0.77	100	empty
3	657	0.71	0.79	74	empty
4	56	0.57	0.90	18	empty
5	106	0.50	0.81	18	empty

Interfaces

9 interfaces between chains.

A–B · 1174 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 1146 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1105 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 452 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 305 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

4RJF · Crystal structure of the human sliding clamp at 2.0 angstrom resolution · the same entry in another collection · chain F against F, TM-score 1.00
P38936 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase inhibitor 1 (P38936) · a predicted model of the same protein · chain F against A, TM-score 0.26

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 P12004
Every structure of UniProt P38936
Elsewhere: RCSB PDB 4RJF · PDBe 4RJF · UniProt P12004 · UniProt P38936

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