SMTL ID : 2plh.1

STRUCTURE OF ALPHA-1-PUROTHIONIN AT ROOM TEMPERATURE AND 2.8 ANGSTROMS RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 1 residues within 4Å: Chain A: R.30 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.30 ACT.2: 4 residues within 4Å: Chain A: S.34, S.35, G.36 Chain C: R.19 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.35, A:G.36, C:R.19 Water bridges: A:S.34 ACT.4: 2 residues within 4Å: Chain A: N.11, L.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.15 Hydrogen bonds: A:N.11 ACT.9: 1 residues within 4Å: Chain B: R.30 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.30 ACT.10: 4 residues within 4Å: Chain A: R.19 Chain B: S.34, S.35, G.36 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.35, B:G.36, A:R.19 Water bridges: B:S.34 ACT.12: 2 residues within 4Å: Chain B: N.11, L.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.15 Hydrogen bonds: B:N.11 ACT.17: 1 residues within 4Å: Chain C: R.30 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.30 ACT.18: 4 residues within 4Å: Chain C: S.34, S.35, G.36 Chain D: R.19 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.35, C:G.36, D:R.19 Water bridges: C:S.34 ACT.20: 2 residues within 4Å: Chain C: N.11, L.15 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.15 Hydrogen bonds: C:N.11 ACT.25: 1 residues within 4Å: Chain D: R.30 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.30 ACT.26: 4 residues within 4Å: Chain B: R.19 Chain D: S.34, S.35, G.36 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.35, D:G.36, B:R.19 Water bridges: D:S.34 ACT.28: 2 residues within 4Å: Chain D: N.11, L.15 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.15 Hydrogen bonds: D:N.11

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 2 residues within 4Å: Chain A: K.1, P.44 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.44, A:P.44 Salt bridges: A:K.1 PO4.11: 2 residues within 4Å: Chain B: K.1, P.44 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.44, B:P.44 Salt bridges: B:K.1 PO4.19: 2 residues within 4Å: Chain C: K.1, P.44 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:P.44, C:P.44 Salt bridges: C:K.1 PO4.27: 2 residues within 4Å: Chain D: K.1, P.44 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.44, D:P.44 Salt bridges: D:K.1

8 x SBT: 2-BUTANOL(Non-covalent)

SBT.5: 3 residues within 4Å: Chain A: T.7, L.8, N.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.8, A:N.11 SBT.6: 3 residues within 4Å: Chain A: S.6, C.29, R.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.29 SBT.13: 3 residues within 4Å: Chain B: T.7, L.8, N.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.8, B:N.11 SBT.14: 3 residues within 4Å: Chain B: S.6, C.29, R.30 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.29 SBT.21: 3 residues within 4Å: Chain C: T.7, L.8, N.11 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.8, C:N.11 SBT.22: 3 residues within 4Å: Chain C: S.6, C.29, R.30 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:C.29 SBT.29: 3 residues within 4Å: Chain D: T.7, L.8, N.11 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.8, D:N.11 SBT.30: 3 residues within 4Å: Chain D: S.6, C.29, R.30 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:C.29

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: K.1, S.2, Y.13, R.17, Q.22 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.2, A:Y.13, A:R.17 Water bridges: A:R.17 GOL.8: 2 residues within 4Å: Chain A: K.1 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.1, A:Q.22 Water bridges: A:Q.22 GOL.15: 6 residues within 4Å: Chain B: K.1, S.2, Y.13, R.17, Q.22 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.2, B:Y.13, B:R.17 Water bridges: B:R.17 GOL.16: 2 residues within 4Å: Chain B: K.1 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.1, B:Q.22 Water bridges: B:Q.22 GOL.23: 6 residues within 4Å: Chain C: K.1, S.2, Y.13, R.17, Q.22 Ligands: GOL.24 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.2, C:Y.13, C:R.17 Water bridges: C:R.17 GOL.24: 2 residues within 4Å: Chain C: K.1 Ligands: GOL.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.1, C:Q.22 Water bridges: C:Q.22 GOL.31: 6 residues within 4Å: Chain D: K.1, S.2, Y.13, R.17, Q.22 Ligands: GOL.32 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.2, D:Y.13, D:R.17 Water bridges: D:R.17 GOL.32: 2 residues within 4Å: Chain D: K.1 Ligands: GOL.31 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.1, D:Q.22 Water bridges: D:Q.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rao, U. et al., Refinement of purothionins reveals solute particles important for lattice formation and toxicity. Part 1: alpha1-purothionin revisited. Acta Crystallogr.,Sect.D (1995)

Release Date

1996-04-03

Peptides

ALPHA-1-PUROTHIONIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

ALPHA-1-PUROTHIONIN