MolNFT v1 · #2046 · protein

Oxalate-substituted diferric lactoferrin

1BKA: “Oxalate-substituted diferric lactoferrin”. X-ray diffraction, 2 ligands (OXL, FE), 9 pockets (best druggability 0.78). MolNFT v1 #2046 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1BKA
Type: protein
Length: 688 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactoferrin
UniProt: P02788
Ligands: OXL, FE
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lactoferrin	protein	688	35% helix, 18% strand	P02788

Ligands and binding sites

OXL · Oxalate ion · ligand · 2 copies · chains A
FE · Fe (III) ion · metal · 2 copies · chains A

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

Pockets

9 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	257	0.78	0.91	44	OXL
2	300	0.76	0.88	38	empty
3	228	0.61	0.81	26	empty
4	255	0.55	0.77	47	empty
5	212	0.50	0.76	31	empty

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

1BKA · Oxalate-substituted diferric lactoferrin · the same entry in another collection · chain A against A, TM-score 1.00
P02788 · AlphaFold monomer V2.0 prediction for lactotransferrin (P02788) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P02788
Elsewhere: RCSB PDB 1BKA · PDBe 1BKA · UniProt P02788

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