Research workbench

Orc-DNA: human origin recognition complex (orc) with DNA bound in the core

Analyse Orc-DNA: human origin recognition complex (orc) with DNA bound in the core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JPS
Type: protein + DNA
Length: 1,958 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Origin recognition complex subunit 1; Origin recognition complex subunit 2; Origin…
UniProt: Q13415, Q13416, Q9UBD5, O43929, O43913
Ligands: ATP, MG, K
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 7 distinct chains · 54% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Origin recognition complex subunit 1	protein	351	53% helix, 9% strand	Q13415
B	Origin recognition complex subunit 2	protein	199	41% helix, 14% strand	Q13416
C	Origin recognition complex subunit 3	protein	591	62% helix, 5% strand	Q9UBD5
D	Origin recognition complex subunit 4	protein	405	56% helix, 7% strand	O43929
E	Origin recognition complex subunit 5	protein	386	50% helix, 9% strand	O43913
F	DNA (5'-D(APTPAPTPAPTPAPTPAPTPAPAP*T)-3')	dna	13	—	—
G	DNA (5'-D(APTPTPAPTPAPTPAPTPAPTPAP*T)-3')	dna	13	—	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, E
MG · Magnesium ion · metal · 3 copies · chains A, D, E
K · Potassium ion · metal · chains B

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	395	0.84	0.93	47	empty
2	1083	0.84	0.85	89	empty
3	1150	0.83	0.84	89	ATP, MG
4	661	0.78	0.83	59	ATP, MG
5	563	0.78	0.84	75	empty

Interfaces

18 interfaces between chains.

B–C · 3585 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 2793 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 2748 Å² buried · 26 hydrogen bonds · protein-protein
C–E · 1888 Å² buried · 19 hydrogen bonds · protein-protein
B–E · 766 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7JPS · ORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in the core · the same entry in another collection · chain C against C, TM-score 1.00
Q13415 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 1 (Q13415) · a predicted model of the same protein · chain A against A, TM-score 0.98
Q9UBD5 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 3 (Q9UBD5) · a predicted model of the same protein · chain C against A, TM-score 0.98
Q13416 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 2 (Q13416) · a predicted model of the same protein · chain B against A, TM-score 0.96
O43929 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 4 (O43929) · a predicted model of the same protein · chain D against A, TM-score 0.93
O43913 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 5 (O43913) · a predicted model of the same protein · chain E against A, TM-score 0.93

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 Q13415
Every structure of UniProt Q13416
Every structure of UniProt Q9UBD5
Every structure of UniProt O43929
Every structure of UniProt O43913
Elsewhere: RCSB PDB 7JPS · PDBe 7JPS · UniProt Q13415 · UniProt Q13416 · UniProt Q9UBD5 · UniProt O43929 · UniProt O43913

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