MolNFT v1 · #109911 · protein

Crystal structure analysis of novel iron uptake mechanism of gram- negative bacterial ferritin

4XGS: “Crystal structure analysis of novel iron uptake mechanism of gram- negative bacterial ferritin”. X-ray diffraction, 2 ligands (OFO, SO4), 8 pockets (best druggability 0.67). MolNFT v1 #109911 on GenesisL1: 3D structure, binding…

PDB: 4XGS
Type: protein
Length: 980 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin
EC: 1.16.3.2
UniProt: P0A998
Ligands: OFO, SO4
Pockets: 8 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 78% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E, F	Ferritin (EC 1.16.3.2)	protein	163	78% helix, 1% strand	P0A998
B, C	Ferritin (EC 1.16.3.2)	protein	164	79% helix, 1% strand	P0A998

Ligands and binding sites

OFO · Hydroxy diiron-oxo moiety · ligand · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 4 copies · chains A, F, C, D, B, E
GOL · Glycerol · additive · 22 copies · chains A, F, B, E, C, D

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	477	0.67	0.79	48	GOL
2	395	0.63	0.78	42	GOL
3	142	0.54	0.81	26	GOL
4	118	0.53	0.82	22	GOL
5	128	0.53	0.81	21	GOL

Interfaces

8 interfaces between chains.

C–D · 1225 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 1194 Å² buried · 11 hydrogen bonds · protein-protein
B–E · 1181 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 456 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 446 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4XGS · Crystal structure analysis of novel iron uptake mechanism of Gram-negative bacterial… · the same entry in another collection · chain F against F, TM-score 1.00
P0A998 · AlphaFold monomer V2.0 prediction for bacterial non-heme ferritin (P0A998) · a predicted model of the same protein · chain E against A, TM-score 0.99

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 P0A998
Elsewhere: RCSB PDB 4XGS · PDBe 4XGS · UniProt P0A998

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