SMTL ID : 3beu.1

Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: H.37, Q.170, G.171, S.173 Ligands: BEN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.171, A:S.173, A:S.173 Salt bridges: A:H.37 SO4.5: 4 residues within 4Å: Chain A: Y.161, D.162, T.163, K.164 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.162, A:T.163, A:K.164 Water bridges: A:T.163 SO4.6: 3 residues within 4Å: Chain A: A.133, N.134, E.166 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.134, A:E.166 Water bridges: A:K.164, A:K.164 Salt bridges: A:K.164 SO4.7: 10 residues within 4Å: Chain A: V.39, S.40, N.45, S.47, I.48 Chain B: S.40, N.45, S.47, I.48 Ligands: BEN.8 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.40, B:N.45, B:N.45, A:S.40, A:S.40, A:N.45 Water bridges: B:S.40, B:S.40, B:S.47, B:S.47 SO4.10: 4 residues within 4Å: Chain A: T.68, K.69, K.89, L.224 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.68 Water bridges: A:K.69, A:K.89 Salt bridges: A:K.69, A:K.89 SO4.11: 4 residues within 4Å: Chain A: G.110, T.111, R.179, K.180 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.111, A:K.180 Water bridges: A:T.111, A:R.179, A:K.180 Salt bridges: A:R.179 SO4.12: 6 residues within 4Å: Chain B: H.37, Q.170, G.171, S.173 Ligands: BEN.8, BEN.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.171, B:S.173, B:S.173 Salt bridges: B:H.37 SO4.16: 3 residues within 4Å: Chain A: R.66 Chain B: G.41, S.42 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.42 Water bridges: B:Q.72, B:Q.72, B:G.75, A:R.66, A:R.66, A:R.66 Salt bridges: A:R.66 SO4.17: 2 residues within 4Å: Chain B: Y.161, D.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.162 SO4.18: 1 residues within 4Å: Chain B: K.100 4 PLIP interactions: 4 interactions with chain B Water bridges: B:T.98, B:T.98, B:T.98, B:E.185 SO4.19: 5 residues within 4Å: Chain A: G.41, S.42, Q.72 Chain B: S.47, R.66 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Water bridges: B:T.49, B:R.66, A:S.42 Salt bridges: B:R.66 Hydrogen bonds: A:S.42, A:Q.72

4 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 13 residues within 4Å: Chain A: D.167, T.168, C.169, Q.170, S.173, V.192, S.193, W.194, G.195, G.197, C.198, G.205 Ligands: SO4.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.192 Hydrogen bonds: A:D.167, A:T.168, A:G.197 Water bridges: A:D.167, A:V.206 BEN.8: 9 residues within 4Å: Chain A: M.20, H.37, C.38 Chain B: M.20, C.22, H.37, C.38 Ligands: SO4.7, SO4.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.20, A:M.20 Hydrogen bonds: B:M.20, B:H.37 BEN.9: 6 residues within 4Å: Chain A: G.43, N.44, K.69, V.70, T.223, L.224 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.69, A:K.69, A:L.224 Hydrogen bonds: A:N.44 Water bridges: A:N.44, A:K.69, A:K.69, A:T.223 BEN.13: 13 residues within 4Å: Chain B: D.167, T.168, C.169, Q.170, S.173, V.192, S.193, W.194, G.195, G.197, C.198, G.205 Ligands: SO4.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.192 Hydrogen bonds: B:D.167, B:T.168, B:T.168, B:G.197 Water bridges: B:V.206

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

NA.3: 5 residues within 4Å: Chain A: Y.161, D.162, R.200, G.202, K.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.161, A:G.202, A:K.203 NA.14: 5 residues within 4Å: Chain B: Y.161, D.162, R.200, G.202, K.203 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.162, B:G.202, B:K.203

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.140, A.153, M.156, E.209 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.140, A:D.140, A:A.153, A:M.156, H2O.1 CA.15: 4 residues within 4Å: Chain B: D.140, A.153, M.156, E.209 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.140, B:D.140, B:A.153, B:M.156, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Page, M.J. et al., Engineering protein allostery: 1.05 A resolution structure and enzymatic properties of a Na+-activated trypsin. J.Mol.Biol. (2008)

Release Date

2008-03-11

Peptides

Trypsin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trypsin