SMTL ID : 3hwg.1 (2 other biounits)

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-TrenCam-hopo2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 3 residues within 4Å: Chain A: Y.126, K.154 Ligands: QED.2 No protein-ligand interaction detected (PLIP)

1 x QED: N,N'-{[(2-{[(2,3-dihydroxyphenyl)carbonyl]amino}ethyl)imino]diethane-2,1-diyl}bis(1-hydroxy-6-oxo-1,6-dihydropyridine-2 -carboxamide)(Non-covalent)

QED.2: 18 residues within 4Å: Chain A: A.60, I.61, Y.72, S.88, L.90, W.99, R.101, L.114, Y.120, L.123, Y.126, F.143, K.145, Y.152, K.154 Ligands: FE.1, SO4.13, SO4.14 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.72, A:L.90, A:L.114, A:Y.120, A:L.123, A:F.143, A:K.145, A:K.145, A:Y.152, A:K.154 Hydrogen bonds: A:K.145, A:K.154 pi-Stacking: A:W.99 pi-Cation interactions: A:K.145

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: N.184, H.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.184 GOL.4: 3 residues within 4Å: Chain A: P.32, L.33, S.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.33, A:S.34, A:S.34 GOL.5: 2 residues within 4Å: Chain A: N.134, H.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.134 GOL.6: 2 residues within 4Å: Chain A: T.165, S.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.166, A:S.166 GOL.7: 3 residues within 4Å: Chain A: K.50, Y.52, D.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.50, A:K.50, A:Y.52

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

NA.8: 1 residues within 4Å: Chain A: S.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.25, A:S.25 NA.9: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.183 NA.10: 4 residues within 4Å: Chain A: R.101, T.102, G.115, Y.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.102, A:T.102, A:Y.120 NA.11: 2 residues within 4Å: Chain A: T.113, Y.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.113, A:Y.126, A:Y.126

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 4 residues within 4Å: Chain A: V.89, Y.98, C.195, G.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.98, A:G.198 SO4.13: 6 residues within 4Å: Chain A: L.56, I.61, Y.72, K.154 Ligands: QED.2, SO4.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.72 Salt bridges: A:K.154 SO4.14: 10 residues within 4Å: Chain A: Y.72, T.74, S.88, R.101, F.143, K.154, T.156, Y.158 Ligands: QED.2, SO4.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.74, A:S.88, A:Y.158 Salt bridges: A:R.101, A:K.154

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

2010-06-02

Peptides

Neutrophil gelatinase-associated lipocalin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neutrophil gelatinase-associated lipocalin

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