Research workbench

Saccharomyces cerevisiae origin recognition complex bound to a 72-bp origin DNA containing acs and B1 element

Analyse Saccharomyces cerevisiae origin recognition complex bound to a 72-bp origin DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZR1
Type: protein + DNA
Length: 2,591 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Origin recognition complex subunit 1; Origin recognition complex subunit 2; Origin…
UniProt: P54784, P32833, P54790, P54791, P50874, P38826
Ligands: AGS, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 8 distinct chains · 48% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Origin recognition complex subunit 1	protein	494	43% helix, 13% strand	P54784
B	Origin recognition complex subunit 2	protein	374	46% helix, 10% strand	P32833
C	Origin recognition complex subunit 3	protein	583	46% helix, 8% strand	P54790
D	Origin recognition complex subunit 4	protein	438	54% helix, 9% strand	P54791
E	Origin recognition complex subunit 5	protein	460	46% helix, 9% strand	P50874
F	Origin recognition complex subunit 6	protein	160	65% helix, 1% strand	P38826
G	72BP-oring DNA, ACS305, T-rich	dna	41	—	—
H	72BP-oring DNA, ACS305, a-rich	dna	41	—	—

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 3 copies · chains A, D, E
MG · Magnesium ion · metal · 3 copies · chains A, D, E

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	363	0.86	0.95	47	empty
2	1186	0.84	0.85	83	AGS, MG
3	475	0.83	0.90	65	empty
4	960	0.83	0.84	76	empty
5	326	0.79	0.90	60	empty

Interfaces

24 interfaces between chains.

B–C · 5606 Å² buried · 59 hydrogen bonds · protein-protein
A–D · 4581 Å² buried · 60 hydrogen bonds · protein-protein
D–E · 3265 Å² buried · 27 hydrogen bonds · protein-protein
C–E · 2366 Å² buried · 20 hydrogen bonds · protein-protein
C–F · 1846 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5ZR1 · Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA… · the same entry in another collection · chain H against H, TM-score 1.00
P54791 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 4 (P54791) · a predicted model of the same protein · chain D against A, TM-score 0.94
P54790 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 3 (P54790) · a predicted model of the same protein · chain C against A, TM-score 0.89
P54784 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 1 (P54784) · a predicted model of the same protein · chain A against A, TM-score 0.83
P38826 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 6 (P38826) · a predicted model of the same protein · chain F against A, TM-score 0.75

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 P54784
Every structure of UniProt P32833
Every structure of UniProt P54790
Every structure of UniProt P54791
Every structure of UniProt P50874
Every structure of UniProt P38826
Elsewhere: RCSB PDB 5ZR1 · PDBe 5ZR1 · UniProt P54784 · UniProt P32833 · UniProt P54790 · UniProt P54791 · UniProt P50874 · UniProt P38826

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