SMTL ID : 3sp8.2 (2 other biounits)

Crystal structure of NK2 in complex with fractionated Heparin DP10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.1: 6 residues within 4Å: Chain A: K.18, R.195, L.197, D.231, Y.234, R.236 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.197, A:Y.234 Hydrogen bonds: A:D.231 MRD.4: 3 residues within 4Å: Chain A: T.23, E.86, F.87 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.23 MRD.5: 1 residues within 4Å: Chain A: F.87 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.87

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 6 residues within 4Å: Chain A: D.239, Q.241, W.245, Y.247, R.254, W.255 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.239, A:R.254 MES.3: 6 residues within 4Å: Chain A: F.137, E.158, W.163, F.165, R.172, Y.173 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.172 Salt bridges: A:E.158, A:R.172 pi-Cation interactions: A:Y.173

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 6 residues within 4Å: Chain A: T.24, L.25, I.26, K.27, L.72, F.74 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.27, A:L.72 Hydrogen bonds: A:T.24

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

SO4.7: 6 residues within 4Å: Chain A: K.37, V.39, R.48, R.51, W.73 Ligands: SO4.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.51 Salt bridges: A:K.37, A:R.48 SO4.8: 2 residues within 4Å: Chain A: K.37, K.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.38 SO4.9: 4 residues within 4Å: Chain A: K.35, K.37, R.48 Ligands: SO4.7 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.35, A:K.37, A:R.48 SO4.10: 3 residues within 4Å: Chain A: R.217, H.218, K.219 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.254 Salt bridges: A:R.217 SO4.11: 1 residues within 4Å: Chain A: R.109 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.109 SO4.12: 2 residues within 4Å: Chain A: R.109, S.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.110, A:S.110 Salt bridges: A:R.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Recacha, R. et al., Crystal structure of NK2 in complex with fractionated Heparin DP10. TO BE PUBLISHED

Release Date

2012-07-04

Peptides

Hepatocyte growth factor alpha chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hepatocyte growth factor alpha chain

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