Research workbench

2.05 a resolution structure of transferrin 1 from manduca sexta

Analyse 2.05 a resolution structure of transferrin 1 from manduca sexta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WB6
Type: protein
Length: 1,306 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transferrin
UniProt: P22297
Ligands: NAG, FE, CO3
Pockets: 17 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transferrin	protein	653	36% helix, 20% strand	P22297
B	Transferrin	protein	653	36% helix, 19% strand	P22297

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
FE · Fe (III) ion · metal · 2 copies · chains A, B
CO3 · Carbonate ion · ion · 4 copies · chains A, B
PG4 · Tetraethylene glycol · additive · chains B

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

Pockets

17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	752	0.68	0.75	75	FE, CO3
2	467	0.66	0.78	42	empty
3	404	0.65	0.79	45	empty
4	503	0.63	0.76	40	FE, CO3
5	113	0.46	0.79	22	empty

Interfaces

1 interface between chains.

A–B · 1183 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6WB6 · 2.05 A resolution structure of transferrin 1 from Manduca sexta · the same entry in another collection · chain A against A, TM-score 1.00
P22297 · AlphaFold monomer V2.0 prediction for transferrin (P22297) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P22297
Elsewhere: RCSB PDB 6WB6 · PDBe 6WB6 · UniProt P22297

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