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Crystal structure of the complex of proliferating cell nuclear antigen from leishmania donovani with arginine at 3.19 a resolution.

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PDB: 6K2M
Type: protein
Length: 1,501 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proliferating cell nuclear antigen
UniProt: B5TV91
Ligands: ARG
Pockets: 10 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, F	Proliferating cell nuclear antigen	protein	248	19% helix, 45% strand	B5TV91
D	Proliferating cell nuclear antigen	protein	251	20% helix, 43% strand	B5TV91
E	Proliferating cell nuclear antigen	protein	258	17% helix, 44% strand	B5TV91

Ligands and binding sites

ARG · Arginine · ligand · 2 copies · chains A, E

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

Pockets

10 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	724	0.68	0.76	66	empty
2	246	0.61	0.81	47	empty
3	363	0.59	0.76	37	empty
4	316	0.55	0.75	30	empty
5	170	0.45	0.75	21	empty

Interfaces

11 interfaces between chains.

D–F · 723 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 696 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 693 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 666 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 656 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6K2M · Crystal structure of the complex of Proliferating Cell Nuclear Antigen from Leishmania… · the same entry in another collection · chain C against C, 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 B5TV91
Elsewhere: RCSB PDB 6K2M · PDBe 6K2M · UniProt B5TV91

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