Research workbench

Human MCM8 N-terminal domain

Analyse Human MCM8 N-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DP3
Type: protein
Length: 557 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA helicase MCM8
EC: 3.6.4.12
UniProt: Q9UJA3
Ligands: ZN
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA helicase MCM8 (EC 3.6.4.12)	protein	278	27% helix, 28% strand	Q9UJA3
B	DNA helicase MCM8 (EC 3.6.4.12)	protein	279	23% helix, 28% strand	Q9UJA3

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	864	0.76	0.79	69	empty
2	638	0.74	0.80	60	empty
3	149	0.55	0.81	23	empty
4	115	0.50	0.81	18	empty
5	99	0.42	0.78	16	empty

Interfaces

1 interface between chains.

A–B · 1063 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7DP3 · Human MCM8 N-terminal domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9UJA3 · AlphaFold monomer V2.0 prediction for DNA helicase MCM8 (Q9UJA3) · a predicted model of the same protein · chain A against A, TM-score 0.83

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 Q9UJA3
Elsewhere: RCSB PDB 7DP3 · PDBe 7DP3 · UniProt Q9UJA3

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