SMTL ID : 4c4n.1

Crystal structure of the Sonic Hedgehog-heparin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

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

IDS-SGN-IDS-SGN-IDS-SGN.1: 5 residues within 4Å: Chain A: K.51, R.87, R.117, R.119, K.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.51, A:R.87, A:R.87, A:R.87 Salt bridges: A:K.51, A:R.117, A:R.87

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

SGN-IDS-SGN-IDS-SGN-IDS.2: 6 residues within 4Å: Chain B: K.51, R.87, T.89, R.117, R.119, K.142 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.142

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.104, D.111, E.140, H.146 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.104, A:D.111, A:D.111, A:H.146 ZN.6: 4 residues within 4Å: Chain B: H.104, D.111, E.140, H.146 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.104, B:D.111, B:D.111, B:H.146, H2O.3

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: E.54, E.90, D.93, D.95, H.97 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.54, A:E.90, A:D.93, A:D.95, H2O.1 CA.5: 5 residues within 4Å: Chain A: E.53, E.54, D.59, T.89, E.90 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.53, A:E.54, A:D.59, A:T.89, A:E.90 CA.7: 5 residues within 4Å: Chain B: E.53, E.54, D.59, T.89, E.90 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.53, B:E.54, B:D.59, B:T.89, B:E.90 CA.8: 4 residues within 4Å: Chain B: E.54, E.90, D.93, D.95 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.54, B:E.90, B:D.93, B:D.95, H2O.3

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

CL.9: 6 residues within 4Å: Chain A: Y.44 Chain B: R.32, T.56, G.57, A.58, L.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whalen, D.M. et al., Structural Insights Into Proteoglycan-Shaped Hedgehog Signaling. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-10-02

Peptides

SONIC HEDGEHOG PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SONIC HEDGEHOG PROTEIN

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