MolNFT v1 · #81958 · protein

The 2.1 ångström crystal structure of diferric human transferrin

3V83 · Serotransferrin: “The 2.1 ångström crystal structure of diferric human transferrin”. X-ray diffraction, 3 ligands (BCT, FE, SO4), 20 pockets (best druggability 0.84). MolNFT v1 #81958 on GenesisL1: 3D structure, binding sites and…

PDB: 3V83
Type: protein
Length: 4,050 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serotransferrin
UniProt: P02787
Ligands: BCT, FE, SO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Serotransferrin	protein	674	36% helix, 19% strand	P02787
B	Serotransferrin	protein	677	37% helix, 19% strand	P02787
D	Serotransferrin	protein	675	36% helix, 19% strand	P02787
F	Serotransferrin	protein	676	37% helix, 19% strand	P02787

Ligands and binding sites

BCT · Bicarbonate ion · ligand · 12 copies · chains A, B, C, D, E, F
FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 44 copies · chains A, D, B, F, C, E
P6G · Hexaethylene glycol · additive · 14 copies · chains A, E, B, C, D, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1110	0.84	0.85	112	empty
2	1130	0.83	0.84	127	SO4
3	1157	0.80	0.81	78	SO4, P6G
4	1017	0.79	0.80	76	SO4
5	151	0.76	0.94	31	empty

Interfaces

9 interfaces between chains.

A–E · 1092 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 1044 Å² buried · 18 hydrogen bonds · protein-protein
C–F · 963 Å² buried · 11 hydrogen bonds · protein-protein
B–F · 859 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 695 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 114 disulfide (disulfide).

Compared structures

3V83 · The 2.1 angstrom crystal structure of diferric human transferrin · the same entry in another collection · chain F against F, TM-score 1.00
P02787 · AlphaFold monomer V2.0 prediction for serotransferrin (P02787) · a predicted model of the same protein · chain B 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 P02787
Elsewhere: RCSB PDB 3V83 · PDBe 3V83 · UniProt P02787

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