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Crystal structure of frog M ferritin mutant D80K

Analyse Crystal structure of frog M ferritin mutant D80K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4P18
Type: protein
Length: 4,128 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin, middle subunit
EC: 1.16.3.1
UniProt: P07798
Ligands: CL, SO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 73% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, M, N, O, P, S, T, E, F, G, H, I, J, K, L, Q, R, U, V, W, X	Ferritin, middle subunit (EC 1.16.3.1)	protein	172	73% helix, 1% strand	P07798

Ligands and binding sites

CL · Chloride ion · ion · 31 copies · chains B, C, D, F, M, O, W, S, G, T, E, H, Q, I, J, L, K, U, V, X
SO4 · Sulfate ion · ion · 25 copies · chains A, B, C, D, N, P, F, W, M, O, T, J, S, G, H, E, I, K, Q, U, L, X, R, V
EDO · 1,2-ethanediol · additive · 51 copies · chains A, R, B, M, C, F, D, N, W, O, P, S, J, T, E, G, I, Q, K, H, L, X, U, V
ACT · Acetate ion · additive · 2 copies · chains A, M, Q, R

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	150	0.80	0.96	28	empty
2	166	0.79	0.95	27	empty
3	210	0.79	0.93	33	empty
4	182	0.78	0.93	29	empty
5	146	0.78	0.94	27	empty

Interfaces

72 interfaces between chains.

W–X · 1465 Å² buried · 20 hydrogen bonds · protein-protein
E–I · 1463 Å² buried · 23 hydrogen bonds · protein-protein
S–T · 1461 Å² buried · 23 hydrogen bonds · protein-protein
U–V · 1458 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1456 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

4P18 · Crystal Structure of frog M ferritin mutant D80K · 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 P07798
Elsewhere: RCSB PDB 4P18 · PDBe 4P18 · UniProt P07798

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