SMTL ID : 3ldi.1

Crystal structure of aprotinin in complex with sucrose octasulfate: unusual interactions and implication for heparin binding

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-10-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: F.4, E.7, K.41, R.42 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: I.18, R.20, K.46 Chain B: I.19 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: P.2 Chain J: P.2, D.3 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.42 Chain J: R.1, P.2 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain B: E.7, K.41, R.42 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain B: I.18, R.20, K.46 Ligand excluded by PLIP SO4.8: 1 residues within 4Å: Chain B: R.42 Ligand excluded by PLIP SO4.9: 8 residues within 4Å: Chain B: C.14, C.38, R.39 Chain C: P.9, F.22, T.32, F.33 Ligands: GOL.10 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain C: F.4, E.7, K.41, R.42 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain C: I.18, R.20, K.46 Chain D: I.19 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain D: E.7, K.41, R.42 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain D: I.18, R.20, K.46 Chain E: I.19 Ligand excluded by PLIP SO4.18: 8 residues within 4Å: Chain C: K.46 Chain D: Y.21, S.47, A.48 Chain H: Y.21, S.47, A.48, E.49 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain D: D.3, R.42 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain E: E.7, K.41, R.42 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain A: I.19 Chain E: I.18, R.20, K.46 Ligand excluded by PLIP SO4.23: 8 residues within 4Å: Chain E: Y.21, S.47, A.48, E.49 Chain F: K.46 Chain G: Y.21, S.47, A.48 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain E: R.42 Chain F: R.1 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain F: F.4, E.7, K.41, R.42 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain F: I.18, R.20, K.46 Chain G: I.19 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain E: P.2, D.3 Chain F: P.2 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain E: R.1, P.2 Chain F: R.42 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain G: E.7, K.41, R.42 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain G: I.18, R.20, K.46 Ligand excluded by PLIP SO4.33: 1 residues within 4Å: Chain G: R.42 Ligand excluded by PLIP SO4.34: 8 residues within 4Å: Chain G: C.14, C.38, R.39 Chain H: P.9, F.22, T.32, F.33 Ligands: GOL.35 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain H: F.4, E.7, K.41, R.42 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain H: I.18, R.20, K.46 Chain I: I.19 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain I: E.7, K.41, R.42 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain I: I.18, R.20, K.46 Chain J: I.19 Ligand excluded by PLIP SO4.43: 8 residues within 4Å: Chain C: Y.21, S.47, A.48, E.49 Chain H: K.46 Chain I: Y.21, S.47, A.48 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain I: D.3, R.42 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain J: E.7, K.41, R.42 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain F: I.19 Chain J: I.18, R.20, K.46 Ligand excluded by PLIP SO4.48: 8 residues within 4Å: Chain A: K.46 Chain B: Y.21, S.47, A.48 Chain J: Y.21, S.47, A.48, E.49 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain A: R.1 Chain J: R.42 Ligand excluded by PLIP

10 x HG: MERCURY (II) ION(Non-covalent)

HG.5: 2 residues within 4Å: Chain A: C.30 Chain F: R.53 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.30 HG.11: 2 residues within 4Å: Chain B: C.30 Chain J: R.53 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.30 HG.15: 2 residues within 4Å: Chain C: C.30 Chain I: R.53 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.30, H2O.3 HG.20: 3 residues within 4Å: Chain D: L.29, C.30 Chain H: R.53 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:C.30 HG.25: 3 residues within 4Å: Chain E: C.30 Chain G: M.52, R.53 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:C.30 HG.30: 2 residues within 4Å: Chain A: R.53 Chain F: C.30 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:C.30 HG.36: 2 residues within 4Å: Chain E: R.53 Chain G: C.30 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:C.30 HG.40: 2 residues within 4Å: Chain D: R.53 Chain H: C.30 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:C.30, H2O.11 HG.45: 3 residues within 4Å: Chain C: R.53 Chain I: L.29, C.30 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:C.30 HG.50: 3 residues within 4Å: Chain B: M.52, R.53 Chain J: C.30 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:C.30

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain B: C.14, C.38, R.39 Ligands: SO4.9 No protein-ligand interaction detected (PLIP) GOL.14: 3 residues within 4Å: Chain C: R.42 Chain H: R.1, P.2 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain H Hydrogen bonds: C:R.42, C:R.42, H:R.1, H:R.1 Water bridges: C:D.3 GOL.35: 4 residues within 4Å: Chain G: C.14, C.38, R.39 Ligands: SO4.34 No protein-ligand interaction detected (PLIP) GOL.39: 3 residues within 4Å: Chain C: R.1, P.2 Chain H: R.42 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain C Hydrogen bonds: H:R.42, H:R.42, C:R.1 Water bridges: H:D.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, I.S. et al., Crystal structures of aprotinin and its complex with sucrose octasulfate reveal multiple modes of interactions with implications for heparin binding. Biochem.Biophys.Res.Commun. (2010)

Release Date

2010-06-23

Peptides

Pancreatic trypsin inhibitor: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

Pancreatic trypsin inhibitor

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