MolNFT v1 · #122728 · protein

Pfmcm N-terminal domain double hexamer

5IY0 · Cell division control protein 21: “Pfmcm N-terminal domain double hexamer”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.68). MolNFT v1 #122728 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IY0
Type: protein
Length: 1,518 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell division control protein 21
UniProt: Q8U3I4
Ligands: ZN
Pockets: 20 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Cell division control protein 21	protein	253	27% helix, 35% strand	Q8U3I4

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	287	0.68	0.83	26	empty
2	278	0.68	0.83	27	empty
3	277	0.68	0.83	30	empty
4	238	0.66	0.84	26	empty
5	299	0.66	0.82	31	empty

Interfaces

6 interfaces between chains.

D–E · 848 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 847 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 842 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 839 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 838 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5IY0 · PfMCM N-terminal domain double hexamer · 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 5IY0 · PDBe 5IY0 · UniProt Q8U3I4

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