SMTL ID : 3k3l.3 (2 other biounits)

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with apo Enterobactin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

monomer

Ligands

1 x MCK: N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2S)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-(L-seryloxy)propanoyl]-L-serine(Non-covalent)

MCK.1: 12 residues within 4Å: Chain A: A.40, I.41, Y.52, L.70, W.79, Y.106, F.123, K.124, K.125, Y.132, F.133, K.134 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.123, A:K.125, A:Y.132, A:K.134, A:K.134 Hydrogen bonds: A:Y.106, A:K.125, A:Y.132, A:K.134 Salt bridges: A:K.125, A:K.134 pi-Stacking: A:W.79, A:W.79

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: T.93, L.94, I.97, S.105, Y.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.94, A:L.94, A:S.105, A:Y.106 GOL.3: 3 residues within 4Å: Chain A: K.59, E.60, D.61 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.60, A:D.61, A:D.61 GOL.4: 4 residues within 4Å: Chain A: K.50, F.71, R.72, K.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.50, A:F.71, A:K.73 GOL.5: 1 residues within 4Å: Chain A: K.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.75, A:K.75 GOL.6: 2 residues within 4Å: Chain A: K.149, F.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.149, A:K.149, A:F.168

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 4 residues within 4Å: Chain A: Y.52, T.54, T.136, Y.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.54, A:Y.138

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 1 residues within 4Å: Chain A: H.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clifton, M.C. et al., Parsing the functional specificity of Siderocalin / Lipocalin 2 / NGAL for siderophores and related small-molecule ligands. To be Published

Release Date

2010-08-18

Peptides

Neutrophil gelatinase-associated lipocalin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Neutrophil gelatinase-associated lipocalin

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