SMTL ID : 4dy0.3 (3 other biounits)

Crystal structure of native protease nexin-1 with heparin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

1 x IDS- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid(Non-covalent)

IDS-SGN.1: 2 residues within 4Å: Chain A: K.74, K.75 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.74, A:K.74 Hydrogen bonds: A:K.74

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

SO4.2: 6 residues within 4Å: Chain A: M.145, I.146, D.147, N.148, K.323, K.325 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.145, A:D.147 Salt bridges: A:K.323, A:K.325 SO4.4: 3 residues within 4Å: Chain B: K.268, R.346, P.350 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.268, B:R.346 SO4.5: 3 residues within 4Å: Chain A: K.302 Chain B: E.241, S.242 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.302 Hydrogen bonds: B:S.242, B:S.243 SO4.6: 3 residues within 4Å: Chain B: D.147, N.148, K.323 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.148 Salt bridges: B:K.323

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: L.159, T.160, K.286, H.316, S.318, H.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.154, A:K.286, A:K.286 GOL.7: 7 residues within 4Å: Chain B: R.269, I.342, L.343, I.344, A.345, R.346, P.349 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.269, B:R.269, B:A.345, B:R.346, B:R.346

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Crystal structures of protease nexin-1 in complex with heparin and thrombin suggest a 2-step recognition mechanism. Blood (2012)

Release Date

2012-08-15

Peptides

Glia-derived nexin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glia-derived nexin

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