Research workbench

Structure of drosophila orc bound to POLY(DA/DT) DNA and CDC6 (conformation 1)

Analyse Structure of drosophila orc bound to POLY(DA/DT) DNA and CDC6 (conformation 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JK2
Type: protein + DNA
Length: 2,589 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Origin recognition complex subunit 2; Origin recognition complex subunit 3; Origin…
UniProt: Q24168, Q7K2L1, Q9W102, Q24169, Q9Y1B2, O16810, Q9VSM9
Ligands: ATP, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 9 distinct chains · 54% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Origin recognition complex subunit 2	protein	285	50% helix, 11% strand	Q24168
C	Origin recognition complex subunit 3	protein	609	58% helix, 6% strand	Q7K2L1
D	Origin recognition complex subunit 4	protein	441	54% helix, 8% strand	Q9W102
E	Origin recognition complex subunit 5	protein	398	51% helix, 11% strand	Q24169
F	Origin recognition complex subunit 6	protein	17	76% helix, 0% strand	Q9Y1B2
A	Origin recognition complex subunit 1	protein	401	52% helix, 10% strand	O16810
G	Cell division control protein	protein	372	52% helix, 10% strand	Q9VSM9
H	DNA (33-mer)	dna	33	—	—
I	DNA (33-mer)	dna	33	—	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains D, E, C, A, G
MG · Magnesium ion · metal · 4 copies · chains D, E, C, A, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1042	0.88	0.90	105	ATP, MG
2	142	0.80	0.97	28	empty
3	958	0.79	0.81	75	empty
4	341	0.77	0.88	42	ATP, MG
5	320	0.77	0.89	45	ATP, MG

Interfaces

24 interfaces between chains.

D–A · 3744 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 3602 Å² buried · 27 hydrogen bonds · protein-protein
D–E · 2821 Å² buried · 28 hydrogen bonds · protein-protein
A–G · 2243 Å² buried · 29 hydrogen bonds · protein-protein
C–E · 2124 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

7JK2 · Structure of Drosophila ORC bound to poly(dA/dT) DNA and Cdc6 (conformation 1) · the same entry in another collection · chain I against I, TM-score 1.00
O16810 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 1 (O16810) · a predicted model of the same protein · chain A against A, TM-score 0.99
Q24169 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 5 (Q24169) · a predicted model of the same protein · chain E against A, TM-score 0.95
Q9Y1B2 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 6 (Q9Y1B2) · a predicted model of the same protein · chain F against A, TM-score 0.79

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 Q24168
Every structure of UniProt Q7K2L1
Every structure of UniProt Q9W102
Every structure of UniProt Q24169
Every structure of UniProt Q9Y1B2
Every structure of UniProt O16810
Every structure of UniProt Q9VSM9
Elsewhere: RCSB PDB 7JK2 · PDBe 7JK2 · UniProt Q24168 · UniProt Q7K2L1 · UniProt Q9W102 · UniProt Q24169 · UniProt Q9Y1B2 · UniProt O16810 · UniProt Q9VSM9

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