SMTL ID : 3qgj.3 (2 other biounits)

1.3A Structure of alpha-Lytic Protease Bound to Ac-AlaAlaPro-Alanal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

4 x ACE- ALA- ALA- PRO- 2A1: Ac-AlaAlaPro-Alanal peptide(Non-covalent)

ACE-ALA-ALA-PRO-2A1.1: 17 residues within 4Å: Chain A: H.36, A.121, N.122, Y.123, E.125, M.138, G.139, R.140, G.141, D.142, S.143, M.158, S.159, G.160, G.161, N.162, V.163 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.123, A:V.163 Hydrogen bonds: A:R.140, A:G.141, A:S.143, A:S.159, A:G.161, A:G.161 ACE-ALA-ALA-PRO-2A1.12: 17 residues within 4Å: Chain B: H.36, A.121, N.122, Y.123, E.125, M.138, G.139, R.140, G.141, D.142, S.143, M.158, S.159, G.160, G.161, N.162, V.163 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.123, B:V.163 Hydrogen bonds: B:R.140, B:G.141, B:S.143, B:S.159, B:G.161, B:G.161 ACE-ALA-ALA-PRO-2A1.23: 17 residues within 4Å: Chain C: H.36, A.121, Y.123, E.125, M.138, G.139, R.140, G.141, D.142, S.143, M.158, S.159, G.160, G.161, N.162, V.163 Ligands: EDO.24 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.123, C:Y.123 Hydrogen bonds: C:G.141, C:S.143, C:S.159, C:G.161, C:G.161 Water bridges: C:N.122 ACE-ALA-ALA-PRO-2A1.30: 17 residues within 4Å: Chain D: H.36, A.121, Y.123, E.125, M.138, G.139, R.140, G.141, D.142, S.143, M.158, S.159, G.160, G.161, N.162, V.163 Ligands: EDO.31 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.123, D:Y.123 Hydrogen bonds: D:G.141, D:S.143, D:S.159, D:G.161, D:G.161 Water bridges: D:H.36, D:H.36, D:N.122

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

EDO.2: 5 residues within 4Å: Chain A: G.52, T.53, S.68, L.69, T.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.53, A:L.69 Water bridges: A:T.53 EDO.3: 9 residues within 4Å: Chain A: T.115, Q.133, G.134, N.135, A.174, S.175, R.177 Chain C: V.96, T.115 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.133, A:G.134, C:T.115 EDO.4: 9 residues within 4Å: Chain A: T.115 Chain C: T.115, Q.133, G.134, N.135, A.174, S.175, R.177 Ligands: SO4.26 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.115, C:Q.133, C:G.134, A:T.115 EDO.13: 5 residues within 4Å: Chain B: G.52, T.53, S.68, L.69, T.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.53, B:L.69 EDO.14: 9 residues within 4Å: Chain B: T.115, Q.133, G.134, N.135, A.174, S.175, R.177 Chain D: V.96, T.115 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:T.115, B:Q.133, B:G.134, D:T.115 EDO.15: 9 residues within 4Å: Chain B: T.115 Chain D: T.115, Q.133, G.134, N.135, A.174, S.175, R.177 Ligands: SO4.33 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:T.115, D:Q.133, D:G.134 EDO.24: 4 residues within 4Å: Chain A: N.118 Chain C: N.122 Ligands: ACE-ALA-ALA-PRO-2A1.23, ACE-ALA-ALA-PRO-2A1.23 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.118, C:N.122, C:N.122 EDO.25: 4 residues within 4Å: Chain C: R.64, R.129, R.183, P.186 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.64, C:R.64, C:R.129, C:R.129, C:R.183 Water bridges: C:N.62, C:N.62, C:R.183 EDO.31: 4 residues within 4Å: Chain B: N.118 Chain D: N.122 Ligands: ACE-ALA-ALA-PRO-2A1.30, ACE-ALA-ALA-PRO-2A1.30 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:N.118, D:N.122, D:N.122 EDO.32: 4 residues within 4Å: Chain D: R.64, R.129, R.183, P.186 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.64, D:R.64, D:R.129, D:R.129, D:R.183 Water bridges: D:N.62, D:N.62, D:R.183

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

SO4.5: 4 residues within 4Å: Chain A: R.25 Chain B: T.120, R.129 Chain D: R.129 13 PLIP interactions: 7 interactions with chain D, 5 interactions with chain B, 1 interactions with chain A Water bridges: D:T.120, D:T.120, D:T.120, D:R.129, D:R.129, D:G.130, B:T.120, B:N.122, B:N.122 Salt bridges: D:R.129, B:R.129, A:R.25 Hydrogen bonds: B:T.120 SO4.6: 3 residues within 4Å: Chain A: P.173, A.174, S.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.174, A:S.175, A:S.175 SO4.7: 4 residues within 4Å: Chain A: N.12, N.13, T.43, R.45 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.43 Water bridges: A:N.13, A:R.45 Salt bridges: A:R.45 SO4.8: 9 residues within 4Å: Chain A: N.62, R.64, P.186, Q.190 Chain B: N.62, R.64, P.186, Q.190 Ligands: SO4.19 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:N.62, B:N.62 Water bridges: A:R.64, A:R.64, A:R.64, A:R.64, B:R.64, B:R.64, B:R.64, B:R.64 Salt bridges: A:R.64, B:R.64 SO4.16: 4 residues within 4Å: Chain A: T.120, R.129 Chain B: R.25 Chain C: R.129 13 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B, 6 interactions with chain A Water bridges: C:T.120, C:T.120, C:R.129, C:R.129, C:G.130, A:T.120, A:T.120, A:T.120, A:N.122, A:N.122 Salt bridges: C:R.129, B:R.25, A:R.129 SO4.17: 3 residues within 4Å: Chain B: P.173, A.174, S.175 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.174, B:S.175, B:S.175 SO4.18: 4 residues within 4Å: Chain B: N.12, N.13, T.43, R.45 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.13 Salt bridges: B:R.45 SO4.19: 9 residues within 4Å: Chain A: N.62, R.64, P.186, Q.190 Chain B: N.62, R.64, P.186, Q.190 Ligands: SO4.8 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:N.62, B:N.62 Water bridges: A:R.64, A:R.64, A:R.64, A:R.64, B:R.64, B:R.64, B:R.64, B:R.64 Salt bridges: A:R.64, B:R.64 SO4.26: 8 residues within 4Å: Chain C: N.135, A.136, C.137, I.172, P.173, A.174, R.177 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.174, C:R.177 Water bridges: C:R.177 Salt bridges: C:R.177 SO4.27: 4 residues within 4Å: Chain C: H.36, R.57, F.59, E.125 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.57 Salt bridges: C:H.36, C:R.57 SO4.28: 2 residues within 4Å: Chain C: N.12, N.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.13 Water bridges: C:N.12 SO4.33: 8 residues within 4Å: Chain D: N.135, A.136, C.137, I.172, P.173, A.174, R.177 Ligands: EDO.15 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.174, D:R.177 Water bridges: D:R.177 Salt bridges: D:R.177 SO4.34: 4 residues within 4Å: Chain D: H.36, R.57, F.59, E.125 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.57 Salt bridges: D:H.36, D:R.57 SO4.35: 2 residues within 4Å: Chain D: N.12, N.13 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.13 Water bridges: D:N.12

8 x TFA: trifluoroacetic acid(Non-covalent)

TFA.9: 3 residues within 4Å: Chain A: N.13, R.45, G.48 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.50 Halogen bonds: A:N.13 TFA.10: 1 residues within 4Å: Chain A: T.74 No protein-ligand interaction detected (PLIP) TFA.11: 4 residues within 4Å: Chain A: R.25 Chain B: G.126, A.127, R.129 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.127, B:R.129, B:R.129 TFA.20: 3 residues within 4Å: Chain B: N.13, R.45, G.48 2 PLIP interactions: 2 interactions with chain B Water bridges: B:V.50 Halogen bonds: B:N.13 TFA.21: 1 residues within 4Å: Chain B: T.74 No protein-ligand interaction detected (PLIP) TFA.22: 4 residues within 4Å: Chain A: G.126, A.127, R.129 Chain B: R.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.127, A:R.129, A:R.129 TFA.29: 3 residues within 4Å: Chain C: E.93, K.117, R.183 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.183 TFA.36: 3 residues within 4Å: Chain D: E.93, K.117, R.183 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Everill, P. et al., Substrate Binding Defines Ser195 Position in the Catalytic Triad of Serine Proteases, Not His57 protonation. To be Published

Release Date

2012-02-01

Peptides

Alpha-lytic protease: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
C

D
C

Alpha-lytic protease

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