Research workbench

D. melanogaster cmg-DNA, state 1B

Analyse D. melanogaster cmg-DNA, state 1B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RAX
Type: protein + DNA
Length: 5,087 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA replication licensing factor MCM2; DNA replication licensing factor MCM3; DNA…
EC: 3.6.4.12
UniProt: P49735, Q9XYU1, Q26454, Q9VGW6, Q9V461, Q9XYU0, O96989, Q9W0I7, Q9VQY9, Q9W2V7, Q9VBI1
Ligands: ATP, ADP
Pockets: 20 · best druggability 0.91

Structure

electron microscopy · 13 distinct chains · 30% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	DNA replication licensing factor MCM2 (EC 3.6.4.12)	protein	605	28% helix, 10% strand	P49735
3	DNA replication licensing factor MCM3 (EC 3.6.4.12)	protein	625	26% helix, 10% strand	Q9XYU1
4	DNA replication licensing factor MCM4 (EC 3.6.4.12)	protein	626	27% helix, 11% strand	Q26454
5	DNA replication licensing factor MCM5 (EC 3.6.4.12)	protein	620	30% helix, 8% strand	Q9VGW6
6	DNA replication licensing factor MCM6 (EC 3.6.4.12)	protein	628	27% helix, 6% strand	Q9V461
7	DNA replication licensing factor MCM7 (EC 3.6.4.12)	protein	632	29% helix, 12% strand	Q9XYU0
X	DNA	dna	21	—	—
Y	DNA	dna	8	—	—
A	CDC45L	protein	567	34% helix, 6% strand	O96989
H	IP07275P	protein	195	35% helix, 0% strand	Q9W0I7
L	Probable DNA replication complex gins protein PSF2	protein	185	40% helix, 5% strand	Q9VQY9
M	AT18545P	protein	167	32% helix, 2% strand	Q9W2V7
N	DNA replication complex gins protein SLD5	protein	208	45% helix, 2% strand	Q9VBI1

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains 2, 6, 3, 5
ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains 4, 7, 6, 3

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	991	0.91	0.93	140	empty
2	1130	0.89	0.90	151	ADP
3	908	0.87	0.89	93	empty
4	878	0.87	0.89	102	ATP
5	1141	0.86	0.87	119	empty

Interfaces

32 interfaces between chains.

2–5 · 3612 Å² buried · 32 hydrogen bonds · protein-protein
4–6 · 3549 Å² buried · 36 hydrogen bonds · protein-protein
3–5 · 3401 Å² buried · 38 hydrogen bonds · protein-protein
2–6 · 3398 Å² buried · 36 hydrogen bonds · protein-protein
4–7 · 3094 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent, 3 disulfide (covalent ligand, disulfide).

Compared structures

6RAX · D. melanogaster CMG-DNA, State 1B · the same entry in another collection · chain N against N, 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 P49735
Every structure of UniProt Q9XYU1
Every structure of UniProt Q26454
Every structure of UniProt Q9VGW6
Every structure of UniProt Q9V461
Every structure of UniProt Q9XYU0
Every structure of UniProt O96989
Every structure of UniProt Q9W0I7
Every structure of UniProt Q9VQY9
Every structure of UniProt Q9W2V7
Every structure of UniProt Q9VBI1
Elsewhere: RCSB PDB 6RAX · PDBe 6RAX · UniProt P49735 · UniProt Q9XYU1 · UniProt Q26454 · UniProt Q9VGW6 · UniProt Q9V461 · UniProt Q9XYU0 · UniProt O96989 · UniProt Q9W0I7 · UniProt Q9VQY9 · UniProt Q9W2V7 · UniProt Q9VBI1

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