SMTL ID : 5kk4.1

Crystal Structure of the Plant Defensin NsD7 bound to Phosphatidic Acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: G.13, I.14, I.16 Ligand excluded by PLIP EDO.2: 2 residues within 4Å: Chain A: I.16, T.17 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain B: T.10, F.11, P.12, P.20, C.21, K.23, A.24 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain B: G.13, I.14 Ligands: SO4.5 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain C: S.36, K.37, I.38, L.39, R.40 Ligands: SO4.11, EDO.14 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain C: E.7, S.36, L.39, R.41, L.43 Ligands: SO4.11, EDO.12 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain C: K.5 Chain D: K.5, R.6, E.7, R.41, L.43 Ligands: 44E.17 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain D: R.22, I.26 Ligands: EDO.21, EDO.22 Ligand excluded by PLIP EDO.19: 1 residues within 4Å: Chain D: K.23 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain C: K.2 Chain D: E.7, S.8, N.9 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain D: K.18, P.19, R.22 Ligands: EDO.16, 44E.18, EDO.22 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain D: R.22, K.23, I.26 Ligands: EDO.16, EDO.21 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain E: S.36, K.37, I.38, L.39 Ligands: 44E.24 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain F: K.23, R.27 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain F: K.37, I.38 Ligands: EDO.30, EDO.31 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain F: K.5, H.34, S.36, K.37, L.43 Ligands: 44E.27, EDO.29, EDO.31 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain F: S.36, K.37, I.38, L.39, R.40 Ligands: EDO.29, EDO.30 Ligand excluded by PLIP

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

SO4.3: 2 residues within 4Å: Chain A: K.2, K.5 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.2, A:K.2 Salt bridges: A:K.2, A:K.5 SO4.5: 3 residues within 4Å: Chain B: P.12, G.13 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.13 SO4.9: 5 residues within 4Å: Chain B: I.16, T.17, K.18, P.19 Chain C: K.37 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:K.18 Water bridges: C:K.37, C:K.37 Salt bridges: C:K.37 SO4.11: 6 residues within 4Å: Chain C: K.5, H.34, S.36, L.43 Ligands: EDO.12, EDO.14 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.5, C:H.34 SO4.25: 6 residues within 4Å: Chain D: K.37 Chain E: I.16, T.17, K.18, P.19 Ligands: 44E.18 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:K.18 Water bridges: D:K.37, D:K.37, D:K.37 Salt bridges: D:K.37

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

ACT.4: 5 residues within 4Å: Chain A: S.36, K.37, I.38, L.39, R.40 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.38 Hydrogen bonds: A:I.38, A:L.39 Water bridges: A:S.36, A:S.36 ACT.8: 1 residues within 4Å: Chain B: K.29 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.29 ACT.13: 2 residues within 4Å: Chain C: G.13, I.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.14

6 x 44E: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate(Non-covalent)

44E.10: 11 residues within 4Å: Chain B: K.37, R.40 Chain C: I.16, T.17, K.18, P.19, G.33, H.34, C.35, K.37, R.40 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:T.17, C:H.34 Hydrogen bonds: C:K.18, C:C.35 Water bridges: C:K.37, B:I.16 Salt bridges: C:K.37, C:R.40, B:K.37, B:K.37, B:R.40 44E.17: 12 residues within 4Å: Chain D: K.5, H.34, S.36, K.37, I.38, L.39, R.40, R.41, L.43 Chain E: I.16 Ligands: EDO.15, 44E.18 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:K.37, D:L.39, D:L.43, E:I.16 Hydrogen bonds: D:K.37, D:I.38 Water bridges: D:K.5 Salt bridges: D:K.5, D:H.34, D:K.37 44E.18: 14 residues within 4Å: Chain D: I.16, T.17, K.18, P.19, H.34, C.35, S.36, K.37, R.40 Chain E: K.37, R.40 Ligands: 44E.17, EDO.21, SO4.25 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:K.18, D:P.19, D:H.34, D:K.37 Hydrogen bonds: D:C.35 Water bridges: D:K.37, E:R.40 Salt bridges: D:K.37, D:R.40, E:K.37, E:K.37, E:R.40 44E.24: 10 residues within 4Å: Chain E: K.2, K.5, H.34, S.36, K.37, L.43 Chain F: E.7, L.39, R.41 Ligands: EDO.23 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:K.2 Water bridges: E:K.5, E:K.5 Salt bridges: E:K.2, E:K.2, E:K.5, E:K.5, E:H.34, E:H.34 44E.26: 3 residues within 4Å: Chain F: G.13, I.14, I.16 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:I.14, F:I.14 44E.27: 9 residues within 4Å: Chain F: I.16, T.17, K.18, P.19, H.34, C.35, K.37, R.40 Ligands: EDO.30 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:H.34, F:K.37 Salt bridges: F:K.18, F:K.37, F:R.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kvansakul, M. et al., Binding of phosphatidic acid by NsD7 mediates the formation of helical defensin-lipid oligomeric assemblies and membrane permeabilization. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-10-05

Peptides

NsD7: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

NsD7

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