Research workbench

Crystal structure of PCNA123 heterotrimer.

Analyse Crystal structure of PCNA123 heterotrimer. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NTI
Type: protein
Length: 2,211 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase sliding clamp B; DNA polymerase sliding clamp C; DNA polymerase sliding…
UniProt: P57766, Q97Z84, P57765
Ligands: 7PG, K, BR
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 7 distinct chains · 20% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, G	DNA polymerase sliding clamp B	protein	249	19% helix, 46% strand	P57766
E	DNA polymerase sliding clamp C	protein	244	20% helix, 48% strand	Q97Z84
F, C	DNA polymerase sliding clamp a	protein	244	20% helix, 44% strand	P57765
A	DNA polymerase sliding clamp B	protein	248	19% helix, 46% strand	P57766
B	DNA polymerase sliding clamp C	protein	245	20% helix, 48% strand	Q97Z84
H	DNA polymerase sliding clamp C	protein	246	20% helix, 47% strand	Q97Z84
I	DNA polymerase sliding clamp a	protein	242	19% helix, 45% strand	P57765

Ligands and binding sites

7PG · 2,5,8,11,14,17,20,23-octaoxapentacosan-25-ol · ligand · chains H
K · Potassium ion · metal · chains H
BR · Bromide ion · ion · 54 copies · chains D, E, F, A, B, C, G, H, I

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	1171	0.80	0.81	124	BR
2	1134	0.71	0.75	104	empty
3	397	0.66	0.79	54	BR
4	424	0.62	0.77	44	empty
5	439	0.61	0.76	54	empty

Interfaces

16 interfaces between chains.

G–H · 745 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 728 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 718 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 712 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 684 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2NTI · Crystal structure of PCNA123 heterotrimer. · the same entry in another collection · chain I against I, TM-score 1.00
Q97Z84 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 2 (Q97Z84) · a predicted model of the same protein · chain E 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 P57766
Every structure of UniProt Q97Z84
Every structure of UniProt P57765
Elsewhere: RCSB PDB 2NTI · PDBe 2NTI · UniProt P57766 · UniProt Q97Z84 · UniProt P57765

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.