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

Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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: EB4.8 No protein-ligand interaction detected (PLIP)

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

NA.2: 4 residues within 4Å: Chain A: Y.72, T.74, R.101, Y.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.74, A:R.101, A:Y.158 NA.3: 3 residues within 4Å: Chain A: L.56, Y.72, K.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.72 NA.4: 1 residues within 4Å: Chain A: N.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.134 NA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

SO4.7: 3 residues within 4Å: Chain A: P.182, N.184, H.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.184 Salt bridges: A:H.185

1 x EB4: N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide)(Non-covalent)

EB4.8: 17 residues within 4Å: Chain A: A.60, Y.72, L.90, R.92, W.99, R.101, L.114, Y.120, L.123, Y.126, F.143, S.147, Y.152, F.153, K.154 Ligands: FE.1, GOL.10 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.72, A:L.90, A:W.99, A:L.114, A:Y.120, A:L.123, A:Y.126, A:F.143, A:Y.152, A:K.154 Hydrogen bonds: A:R.92, A:R.92, A:R.101, A:Y.126, A:S.147, A:K.154 pi-Stacking: A:W.99

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: T.113, L.114, I.117, S.125, Y.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.114, A:L.114, A:S.125 GOL.10: 2 residues within 4Å: Chain A: W.99 Ligands: EB4.8 No protein-ligand interaction detected (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

2009-05-12

Peptides

Neutrophil gelatinase-associated lipocalin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Neutrophil gelatinase-associated lipocalin

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