MolNFT v1 · #117110 · protein

TI(IV) bound human serum transferrin

5DYH · Serotransferrin: “TI(IV) bound human serum transferrin”. X-ray diffraction, 2 ligands (4TI, CO3), 14 pockets (best druggability 0.73). MolNFT v1 #117110 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DYH
Type: protein
Length: 1,354 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serotransferrin
UniProt: P02787
Ligands: 4TI, CO3
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Serotransferrin	protein	677	34% helix, 18% strand	P02787

Ligands and binding sites

4TI · Titanium ion · metal · 2 copies · chains A, B
CO3 · Carbonate ion · ion · 2 copies · chains A, B
CIT · Citric acid · additive · 11 copies · chains A, B

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

Pockets

14 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	483	0.73	0.82	43	empty
2	716	0.73	0.79	68	CIT
3	745	0.66	0.74	67	empty
4	526	0.61	0.75	40	empty
5	409	0.59	0.75	41	empty

Interfaces

1 interface between chains.

A–B · 604 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 38 disulfide (disulfide).

Compared structures

5DYH · Ti(IV) bound human serum transferrin · the same entry in another collection · chain A against A, TM-score 1.00
P02787 · AlphaFold monomer V2.0 prediction for serotransferrin (P02787) · a predicted model of the same protein · chain A against A, TM-score 0.70

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 P02787
Elsewhere: RCSB PDB 5DYH · PDBe 5DYH · UniProt P02787

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