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Structure of a sliding clamp on DNA

Analyse Structure of a sliding clamp on DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BEP
Type: protein + DNA
Length: 756 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(P*DCP*DCP*DCP*DAP*DTP*DCP*DGP*DTP*DAP*DT)-3'); DNA (5'…
EC: 2.7.7.7
UniProt: P0A988
Ligands: 5CY
Pockets: 10 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	DNA (5'-D(PDCPDCPDCPDAPDTPDCPDGPDTPDAPDT)-3')	dna	10	—	—
D	DNA (5'- D(DTPDTPDTPDTPDAPDTPDAPDCPDGPDAPDTPDGPDGPDG)-3')	dna	14	—	—
A, B	DNA polymerase III subunit beta (EC 2.7.7.7)	protein	366	22% helix, 47% strand	P0A988

Ligands and binding sites

5CY · 1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-yl}-3,3-dimethyl-3H-indolium · ligand · chains C, D, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1115	0.71	0.75	70	empty
2	939	0.69	0.75	73	empty
3	85	0.34	0.75	17	empty
4	77	0.32	0.74	20	empty
5	57	0.32	0.76	15	empty

Interfaces

6 interfaces between chains.

A–B · 1334 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 449 Å² buried · 33 hydrogen bonds · nucleic-nucleic
D–A · 341 Å² buried · 1 hydrogen bond · protein-nucleic
C–B · 160 Å² buried · 1 hydrogen bond · protein-nucleic
D–B · 89 Å² buried · 1 hydrogen bond · protein-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

3BEP · Structure of a sliding clamp on DNA · the same entry in another collection · chain C against C, TM-score 1.00
P0A988 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P0A988) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P0A988
Elsewhere: RCSB PDB 3BEP · PDBe 3BEP · UniProt P0A988

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