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Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4

Analyse Crystal structure of the processivity clamp GP45 complexed with recognition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DRT
Type: protein
Length: 717 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase clamp; GP45 recognition loop
UniProt: P04525, P00970
Pockets: 6 · best druggability 0.38

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	DNA polymerase clamp	protein	230	18% helix, 41% strand	P04525
B	DNA polymerase clamp	protein	228	18% helix, 41% strand	P04525
D, F	GP45 recognition loop	protein	9	44% helix, 0% strand	P00970
E	GP45 recognition loop	protein	11	36% helix, 0% strand	P00970

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, F

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

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.38	0.79	19	empty
2	67	0.36	0.78	16	empty
3	73	0.34	0.76	13	empty
4	50	0.30	0.77	14	empty
5	50	0.30	0.77	14	empty

Interfaces

6 interfaces between chains.

B–E · 569 Å² buried · 1 hydrogen bond · protein-protein
A–B · 538 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 518 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 515 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 496 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6DRT · Crystal structure of the processivity clamp GP45 complexed with recognition peptide of… · 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 P04525
Every structure of UniProt P00970
Elsewhere: RCSB PDB 6DRT · PDBe 6DRT · UniProt P04525 · UniProt P00970

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