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DNA polymerase sliding clamp from escherichia COLI with peptide 22 bound

Analyse DNA polymerase sliding clamp from escherichia COLI with peptide 22 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AZC
Type: protein
Length: 1,479 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta sliding clamp; Peptide 22
UniProt: A0A073FMV0
Ligands: QU8, GLN
Pockets: 15 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 22% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta sliding clamp	protein	368	22% helix, 45% strand	A0A073FMV0
B	Beta sliding clamp	protein	365	22% helix, 47% strand	A0A073FMV0
C	Beta sliding clamp	protein	366	22% helix, 46% strand	A0A073FMV0
D	Beta sliding clamp	protein	364	22% helix, 47% strand	A0A073FMV0
H, I, J, K	Peptide 22	protein	4	0% helix, 0% strand	—

Ligands and binding sites

QU8 · ~{N}-(4-methoxyphenyl)methanamide · ligand · 4 copies · chains A, C, J, B, D, I, K, H
GLN · Glutamine · ligand · 4 copies · chains A, C, H, B, D, I, J, K
GOL · Glycerol · additive · 2 copies · chains B, I, C

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

Pockets

15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1104	0.70	0.74	98	QU8, GLN
2	911	0.68	0.74	80	QU8, GLN
3	718	0.67	0.75	82	QU8, GLN
4	382	0.55	0.74	43	empty
5	190	0.43	0.73	27	empty

Interfaces

13 interfaces between chains.

C–D · 1319 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1297 Å² buried · 31 hydrogen bonds · protein-protein
C–J · 437 Å² buried · 3 hydrogen bonds · protein-protein
D–K · 434 Å² buried · 2 hydrogen bonds · protein-protein
B–I · 426 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).

Compared structures

7AZC · DNA polymerase sliding clamp from Escherichia coli with peptide 22 bound · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A073FMV0
Elsewhere: RCSB PDB 7AZC · PDBe 7AZC · UniProt A0A073FMV0

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