SMTL ID : 3fw5.1 (2 other biounits)

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

FE.1: 2 residues within 4Å: Chain A: Y.106 Ligands: MCT.2 No protein-ligand interaction detected (PLIP)

1 x MCT: 4-METHYLCATECHOL(Non-covalent)

MCT.2: 9 residues within 4Å: Chain A: A.40, Y.106, F.123, K.124, K.125, Y.132, F.133, K.134 Ligands: FE.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.40, A:K.125, A:Y.132, A:K.134, A:K.134, A:K.134 Hydrogen bonds: A:K.125, A:K.134

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

NA.3: 3 residues within 4Å: Chain A: K.30, Y.32, D.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.32, A:Y.32 NA.4: 1 residues within 4Å: Chain A: S.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.146 NA.5: 1 residues within 4Å: Chain A: K.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.73

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

CL.6: 3 residues within 4Å: Chain A: W.79, R.81, Y.100 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: N.114, Q.117, H.118 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.114 GOL.8: 3 residues within 4Å: Chain A: P.162, N.164, H.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.164 GOL.9: 2 residues within 4Å: Chain A: Q.117 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bao, G. et al., Iron traffics in circulation bound to a siderocalin (Ngal)-catechol complex. Nat.Chem.Biol. (2010)

Release Date

2010-05-05

Peptides

Neutrophil gelatinase-associated lipocalin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neutrophil gelatinase-associated lipocalin

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