MolNFT v1 · #109390 · protein

Ytterbium-bound human serum transferrin

4X1D · Serotransferrin: “Ytterbium-bound human serum transferrin”. X-ray diffraction, 1 ligand (YB), 12 pockets (best druggability 0.77). MolNFT v1 #109390 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4X1D
Type: protein
Length: 1,316 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serotransferrin
UniProt: P02787
Ligands: YB
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Serotransferrin	protein	658	36% helix, 19% strand	P02787

Ligands and binding sites

YB · Ytterbium (III) ion · metal · 2 copies · chains A, B
MLI · Malonate ion · additive · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

12 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	854	0.77	0.81	78	MLI
2	858	0.77	0.80	84	MLI
3	1147	0.76	0.79	97	GOL
4	686	0.76	0.82	64	GOL
5	84	0.48	0.82	17	empty

Interfaces

1 interface between chains.

A–B · 651 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 disulfide (disulfide).

Compared structures

4X1D · Ytterbium-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 0.82

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 4X1D · PDBe 4X1D · UniProt P02787

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