SMTL ID : 2ftm.2 (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-4-4-mer

Ligands

4 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:D.53 NA.17: 2 residues within 4Å: Chain C: D.53, E.59 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.59 NA.33: 2 residues within 4Å: Chain E: D.53, E.59 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.53, E:E.59 NA.49: 2 residues within 4Å: Chain G: D.53, E.59 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.53, G:E.59

36 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: 4 residues within 4Å: Chain A: K.43, S.44 Chain B: K.46 Chain D: 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: 5 residues within 4Å: Chain B: R.1, R.42 Chain C: K.69, K.89, N.223 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: 3 residues within 4Å: Chain B: R.1 Chain C: Q.33, K.89 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain B: R.1 Chain C: Q.33, K.91, S.92, A.93 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: K.149, P.153, G.154 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain B: K.46 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: 5 residues within 4Å: Chain A: K.69, K.89, N.223 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: 3 residues within 4Å: Chain A: Q.33, K.89 Chain D: R.1 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain A: Q.33, K.91, S.92, A.93 Chain D: R.1 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain E: K.149, P.153, G.154 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain E: K.43, S.44 Chain F: K.46 Chain H: K.46 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain E: P.132, D.133, V.134, K.136 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain E: S.75, N.77, N.82, N.83 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain F: F.4, E.7, K.41, R.42 Ligand excluded by PLIP SO4.44: 5 residues within 4Å: Chain F: R.1, R.42 Chain G: K.69, K.89, N.223 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain F: P.9, Y.10, T.11, G.12 Ligands: EDO.40 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain F: R.1 Chain G: Q.33, K.89 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain F: R.1 Chain G: Q.33, K.91, S.92, A.93 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain G: K.149, P.153, G.154 Ligand excluded by PLIP SO4.51: 4 residues within 4Å: Chain F: K.46 Chain G: K.43, S.44 Chain H: K.46 Ligand excluded by PLIP SO4.52: 4 residues within 4Å: Chain G: P.132, D.133, V.134, K.136 Ligand excluded by PLIP SO4.53: 4 residues within 4Å: Chain G: S.75, N.77, N.82, N.83 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain H: F.4, E.7, K.41, R.42 Ligand excluded by PLIP SO4.60: 5 residues within 4Å: Chain E: K.69, K.89, N.223 Chain H: R.1, R.42 Ligand excluded by PLIP SO4.61: 5 residues within 4Å: Chain H: P.9, Y.10, T.11, G.12 Ligands: EDO.56 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain E: Q.33, K.89 Chain H: R.1 Ligand excluded by PLIP SO4.63: 5 residues within 4Å: Chain E: Q.33, K.91, S.92, A.93 Chain H: R.1 Ligand excluded by PLIP

8 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 H: Q.31, T.32 Ligands: CA.64 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 D: Q.31, T.32 Chain F: Q.31, T.32 Ligands: CA.48 No protein-ligand interaction detected (PLIP) CA.38: 4 residues within 4Å: Chain E: E.52, N.54, V.57, E.62 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.52, E:N.54, E:V.57, E:E.62, H2O.21 CA.48: 5 residues within 4Å: Chain D: Q.31, T.32 Chain F: Q.31, T.32 Ligands: CA.32 No protein-ligand interaction detected (PLIP) CA.54: 4 residues within 4Å: Chain G: E.52, N.54, V.57, E.62 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.52, G:N.54, G:V.57, G:E.62, H2O.30 CA.64: 5 residues within 4Å: Chain B: Q.31, T.32 Chain H: Q.31, T.32 Ligands: CA.16 No protein-ligand interaction detected (PLIP)

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

EDO.7: 3 residues within 4Å: Chain A: Y.5, C.7, T.11 Ligand excluded by PLIP 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 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: A.110, I.142, F.161, K.208 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: Q.155, W.193 Chain B: P.13, R.39 Ligands: EDO.8 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain C: Y.5, C.7, T.11 Ligand excluded by PLIP 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 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: A.110, I.142, F.161, K.208 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: Q.155, W.193 Chain D: P.13, R.39 Ligands: EDO.24 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain E: Y.5, C.7, T.11 Ligand excluded by PLIP EDO.40: 8 residues within 4Å: Chain E: G.194, S.195, G.196 Chain F: Y.10, G.12, P.13 Ligands: EDO.42, SO4.45 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain E: A.110, I.142, F.161, K.208 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain E: Q.155, W.193 Chain F: P.13, R.39 Ligands: EDO.40 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain G: Y.5, C.7, T.11 Ligand excluded by PLIP EDO.56: 8 residues within 4Å: Chain G: G.194, S.195, G.196 Chain H: Y.10, G.12, P.13 Ligands: EDO.58, SO4.61 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain G: A.110, I.142, F.161, K.208 Ligand excluded by PLIP EDO.58: 5 residues within 4Å: Chain G: Q.155, W.193 Chain H: P.13, R.39 Ligands: EDO.56 Ligand excluded by PLIP

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: ACEG
Pancreatic trypsin inhibitor: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

Cationic trypsin

Pancreatic trypsin inhibitor

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