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Pyrococcus furiosus mcm N-terminal domain beta-turn triple mutant pentameric ring

Analyse Pyrococcus furiosus mcm N-terminal domain beta-turn triple mutant pentameric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YWM
Type: protein
Length: 2,545 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell division control protein 21
UniProt: Q8U3I4
Ligands: ZN, SO4
Pockets: 20 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Cell division control protein 21	protein	255	29% helix, 35% strand	Q8U3I4
F, G, H, I, J	Cell division control protein 21	protein	254	26% helix, 35% strand	Q8U3I4

Ligands and binding sites

ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
SO4 · Sulfate ion · ion · 8 copies · chains B, D, E, F, G, H, I, J

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	611	0.68	0.77	54	SO4
2	561	0.68	0.78	54	empty
3	554	0.67	0.78	58	empty
4	561	0.67	0.77	58	empty
5	544	0.67	0.78	58	empty

Interfaces

15 interfaces between chains.

C–G · 747 Å² buried · 9 hydrogen bonds · protein-protein
B–F · 746 Å² buried · 9 hydrogen bonds · protein-protein
A–J · 744 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 743 Å² buried · 7 hydrogen bonds · protein-protein
E–I · 737 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4YWM · Pyrococcus furiosus MCM N-terminal domain beta-turn triple mutant pentameric ring · the same entry in another collection · chain A against A, 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 Q8U3I4
Elsewhere: RCSB PDB 4YWM · PDBe 4YWM · UniProt Q8U3I4

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