MolNFT v1 · #57506 · protein

Crystal structure analysis of E173A variant of the soybean ferritin SFER4

3A9Q · Ferritin-4, chloroplastic: “Crystal structure analysis of E173A variant of the soybean ferritin SFER4”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.59). MolNFT v1 #57506 on GenesisL1: 3D structure, binding…

PDB: 3A9Q
Type: protein
Length: 4,629 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin-4, chloroplastic
EC: 1.16.3.1
UniProt: Q948P5
Ligands: CA
Pockets: 20 · best druggability 0.59

Structure

x-ray diffraction · 4 distinct chains · 71% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, J, T, W, X	Ferritin-4, chloroplastic (EC 1.16.3.1)	protein	194	71% helix, 1% strand	Q948P5
E	Ferritin-4, chloroplastic (EC 1.16.3.1)	protein	178	71% helix, 1% strand	Q948P5
G, H, I, K, L, M, N, O, P, Q, S, U, V	Ferritin-4, chloroplastic (EC 1.16.3.1)	protein	193	72% helix, 1% strand	Q948P5
R	Ferritin-4, chloroplastic (EC 1.16.3.1)	protein	196	70% helix, 1% strand	Q948P5

Ligands and binding sites

CA · Calcium ion · metal · 124 copies · chains A, G, B, E, F, C, R, S, D, H, V, I, O, W, J, N, Q, K, P, U, L, M, T, X
ACY · Acetic acid · additive · 18 copies · chains A, E, F, G, H, I, J, L, M, O, P, Q, R, S, T, V, W, X

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	372	0.59	0.76	23	empty
2	352	0.59	0.76	25	empty
3	345	0.59	0.76	27	empty
4	345	0.59	0.76	23	empty
5	353	0.58	0.76	26	empty

Interfaces

73 interfaces between chains.

A–G · 1815 Å² buried · 26 hydrogen bonds · protein-protein
M–S · 1814 Å² buried · 26 hydrogen bonds · protein-protein
J–X · 1812 Å² buried · 26 hydrogen bonds · protein-protein
Q–U · 1808 Å² buried · 28 hydrogen bonds · protein-protein
E–I · 1798 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

3A9Q · Crystal Structure Analysis of E173A variant of the soybean ferritin SFER4 · the same entry in another collection · chain K against K, 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 Q948P5
Elsewhere: RCSB PDB 3A9Q · PDBe 3A9Q · UniProt Q948P5

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