SMTL ID : 2ftm.4 (5 other biounits)

Crystal structure of trypsin complexed with the BPTI variant (Tyr35->Gly)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: D.53, E.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.59 NA.17: 2 residues within 4Å: Chain C: D.53, E.59 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.53, C:D.53

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

SO4.2: 3 residues within 4Å: Chain A: K.149, P.153, G.154 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: K.43, S.44 Chain B: K.46 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: P.132, D.133, V.134, K.136 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: S.75, N.77, N.82, N.83 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: F.4, E.7, K.41, R.42 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain B: R.1, R.42 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain B: P.9, Y.10, T.11, G.12 Ligands: EDO.8 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain B: R.1 Ligand excluded by PLIP SO4.15: 1 residues within 4Å: Chain B: R.1 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: K.149, P.153, G.154 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: K.43, S.44 Chain D: K.46 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: P.132, D.133, V.134, K.136 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain C: S.75, N.77, N.82, N.83 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain D: F.4, E.7, K.41, R.42 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain D: R.1, R.42 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain D: P.9, Y.10, T.11, G.12 Ligands: EDO.24 Ligand excluded by PLIP SO4.30: 1 residues within 4Å: Chain D: R.1 Ligand excluded by PLIP SO4.31: 1 residues within 4Å: Chain D: R.1 Ligand excluded by PLIP

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: E.52, N.54, V.57, E.62 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.52, A:N.54, A:V.57, A:E.62, H2O.2 CA.16: 5 residues within 4Å: Chain B: Q.31, T.32 Chain D: Q.31, T.32 Ligands: CA.32 No protein-ligand interaction detected (PLIP) CA.22: 4 residues within 4Å: Chain C: E.52, N.54, V.57, E.62 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.52, C:N.54, C:V.57, C:E.62, H2O.12 CA.32: 5 residues within 4Å: Chain B: Q.31, T.32 Chain D: Q.31, T.32 Ligands: CA.16 No protein-ligand interaction detected (PLIP)

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 3 residues within 4Å: Chain A: Y.5, C.7, T.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.5, A:C.7, A:T.11 EDO.8: 8 residues within 4Å: Chain A: G.194, S.195, G.196 Chain B: Y.10, G.12, P.13 Ligands: EDO.10, SO4.13 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.196, B:Y.10, B:Y.10, B:G.12 Water bridges: A:Q.174, A:Q.174, A:Q.174 EDO.9: 4 residues within 4Å: Chain A: A.110, I.142, F.161, K.208 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.110 Water bridges: A:D.145, A:M.160, A:K.208 EDO.10: 5 residues within 4Å: Chain A: Q.155, W.193 Chain B: P.13, R.39 Ligands: EDO.8 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.155, B:R.39 Water bridges: A:S.195, B:Y.10, B:Y.10 EDO.23: 3 residues within 4Å: Chain C: Y.5, C.7, T.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:C.7 EDO.24: 8 residues within 4Å: Chain C: G.194, S.195, G.196 Chain D: Y.10, G.12, P.13 Ligands: EDO.26, SO4.29 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.196, D:Y.10, D:G.12 Water bridges: C:Q.174, C:Q.174 EDO.25: 4 residues within 4Å: Chain C: A.110, I.142, F.161, K.208 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.110 Water bridges: C:D.145, C:M.160, C:K.208 EDO.26: 5 residues within 4Å: Chain C: Q.155, W.193 Chain D: P.13, R.39 Ligands: EDO.24 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.155, D:R.39 Water bridges: C:S.195, D:Y.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hanson, W.M. et al., Rigidification of a Flexible Protease Inhibitor Variant upon Binding to Trypsin. J.Mol.Biol. (2007)

Release Date

2006-02-14

Peptides

Cationic trypsin: AC
Pancreatic trypsin inhibitor: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Cationic trypsin

Pancreatic trypsin inhibitor

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