MolNFT v1 · #94918 · protein

Engineered human lipocalin 2 (C26) in complex with Y-dtpa

4IAW · Neutrophil gelatinase-associated lipocalin: “Engineered human lipocalin 2 (C26) in complex with Y-dtpa”. X-ray diffraction, 2 ligands (LIZ, YT3), 6 pockets (best druggability 0.74). MolNFT v1 #94918 on GenesisL1: 3D structure…

PDB: 4IAW
Type: protein
Length: 528 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neutrophil gelatinase-associated lipocalin
UniProt: P80188
Ligands: LIZ, YT3
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neutrophil gelatinase-associated lipocalin	protein	180	17% helix, 42% strand	P80188
B	Neutrophil gelatinase-associated lipocalin	protein	176	16% helix, 43% strand	P80188
C	Neutrophil gelatinase-associated lipocalin	protein	172	13% helix, 40% strand	P80188

Ligands and binding sites

LIZ · N-{(1S,2S)-2-[bis(carboxymethyl)amino]cyclohexyl}-N-{(2R)-2-[bis(carboxymethyl)amino]-3-[4-({[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]carbamothioyl}amino)phenyl]propyl}glycine · ligand · 3 copies · chains A, B, C
YT3 · Yttrium (III) ion · metal · 3 copies · chains A, B, C

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	587	0.74	0.81	47	LIZ, YT3
2	695	0.74	0.80	47	LIZ, YT3
3	681	0.72	0.79	45	LIZ, YT3
4	120	0.42	0.76	16	empty
5	108	0.38	0.75	22	empty

Interfaces

2 interfaces between chains.

A–B · 433 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 224 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4IAW · Engineered human lipocalin 2 (C26) in complex with Y-DTPA · the same entry in another collection · 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 P80188
Elsewhere: RCSB PDB 4IAW · PDBe 4IAW · UniProt P80188

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