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Crystal structure of proliferating cell nuclear antigen 2 and short peptide from human P21

Analyse Crystal structure of proliferating cell nuclear antigen 2 and short peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZVW
Type: protein
Length: 2,128 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proliferating cell nuclear antigen 2; Cyclin-dependent kinase inhibitor 1
UniProt: Q9ZW35, P38936
Ligands: SO4
Pockets: 20 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Proliferating cell nuclear antigen 2	protein	255	21% helix, 45% strand	Q9ZW35
I, J, K, L, M, N, O, P	Cyclin-dependent kinase inhibitor 1	protein	11	27% helix, 9% strand	P38936

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D, E, F, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	147	0.55	0.82	22	empty
2	321	0.54	0.75	56	empty
3	154	0.52	0.80	24	empty
4	98	0.52	0.83	26	empty
5	256	0.51	0.75	34	empty

Interfaces

21 interfaces between chains.

B–C · 789 Å² buried · 13 hydrogen bonds · protein-protein
D–F · 788 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 786 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 786 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 776 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

2ZVW · Crystal structure of Proliferating cell nuclear antigen 2 and Short peptide from human P21 · the same entry in another collection · chain G against G, 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 Q9ZW35
Every structure of UniProt P38936
Elsewhere: RCSB PDB 2ZVW · PDBe 2ZVW · UniProt Q9ZW35 · UniProt P38936

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