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

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-TrenCam2-hopo

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

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

FE.1: 2 residues within 4Å: Chain A: K.154 Ligands: TC2.4 No protein-ligand interaction detected (PLIP)

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

SO4.2: 10 residues within 4Å: Chain A: V.53, Y.72, T.74, S.88, R.101, F.143, K.154, T.156, Y.158 Ligands: TC2.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.88, A:Y.158, A:Y.158 Salt bridges: A:R.101, A:K.154 SO4.3: 4 residues within 4Å: Chain A: T.102, G.115, N.116, Y.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.102, A:T.102, A:T.102

1 x TC2: N-{2-[bis(2-{[(2,3-dihydroxyphenyl)carbonyl]amino}ethyl)amino]ethyl}-1-hydroxy-6-oxo-1,6-dihydropyridine-2-carboxamide(Non-covalent)

TC2.4: 16 residues within 4Å: Chain A: A.60, I.61, Y.72, S.88, L.90, W.99, R.101, Y.120, L.123, Y.126, F.143, K.145, Y.152, K.154 Ligands: FE.1, SO4.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.72, A:L.90, A:Y.120, A:L.123, A:F.143, A:K.145, A:K.145, A:Y.152, A:K.154, A:K.154 Hydrogen bonds: A:R.101, A:Y.126, A:K.145, A:K.145, A:K.145, A:K.154 pi-Stacking: A:W.99, A:W.99 pi-Cation interactions: A:K.145

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

CL.5: 2 residues within 4Å: Chain A: Y.72, K.154 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: N.134, H.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.134 GOL.7: 2 residues within 4Å: Chain A: S.125, Y.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.126 GOL.9: 1 residues within 4Å: Chain A: K.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.95

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

NA.8: 1 residues within 4Å: Chain A: S.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.166, A:S.166

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
C

Neutrophil gelatinase-associated lipocalin

Related Entries With Identical Sequence