SMTL ID : 3s8k.1

Crystal structure of a papaya latex serine protease inhibitor (PPI) at 1.7A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.1: 5 residues within 4Å: Chain A: G.17, D.19, I.61, N.84, N.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.183 Water bridges: A:D.19 NAG-FUC-NAG.2: 4 residues within 4Å: Chain B: G.17, D.19, I.61, N.84 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.19, B:D.19

2 x CO: COBALT (II) ION(Non-covalent)

CO.3: 1 residues within 4Å: Chain A: H.117 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.117, H2O.1, H2O.1 CO.4: 2 residues within 4Å: Chain A: D.52, D.55 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.52, A:D.52, A:D.55, H2O.6

3 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.5: 3 residues within 4Å: Chain A: G.118, F.119, E.120 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.119, A:E.120 Water bridges: A:G.118, A:F.119, A:S.121 NH4.6: 3 residues within 4Å: Chain A: Y.37, G.38, K.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.38, A:K.44 NH4.14: 2 residues within 4Å: Chain B: Y.37, G.38 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.37, B:G.38

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: E.75, S.76, K.129, K.130 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.75, A:S.76, A:K.129, A:K.129, A:K.130 GOL.8: 3 residues within 4Å: Chain A: K.138, N.155, N.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.138, A:N.155 Water bridges: A:D.173, A:A.174 GOL.15: 4 residues within 4Å: Chain B: K.66, S.144, Y.145, P.146 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.66, B:S.144 Water bridges: B:K.66, B:Y.145, B:Y.145 GOL.16: 3 residues within 4Å: Chain B: F.160, R.164, R.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.164, B:R.164, B:R.166

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

SO4.9: 2 residues within 4Å: Chain A: K.66, N.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.67 Salt bridges: A:K.66 SO4.10: 3 residues within 4Å: Chain A: R.99, I.104, G.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105 Water bridges: A:R.99 Salt bridges: A:R.99 SO4.11: 3 residues within 4Å: Chain A: K.43, K.44, C.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.42, A:K.44, A:C.45 SO4.12: 4 residues within 4Å: Chain A: K.127, K.129, H.140, C.142 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.127, A:K.127, A:H.140 Salt bridges: A:K.127, A:K.129 SO4.13: 2 residues within 4Å: Chain A: T.148, R.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.149 SO4.17: 3 residues within 4Å: Chain B: K.43, K.44, C.45 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.44, B:C.45 Water bridges: B:K.44 Salt bridges: B:K.44 SO4.18: 4 residues within 4Å: Chain B: R.99, G.105, W.106, P.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.106 Salt bridges: B:R.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Azarkan, M. et al., The plasticity of the beta-Trefoil fold constitutes an evolutionary platform for protease inhibition. J.Biol.Chem. (2011)

Release Date

2011-11-02

Peptides

Latex serine proteinase inhibitor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Latex serine proteinase inhibitor

Related Entries With Identical Sequence