SMTL ID : 6b55.1

Crystal structure of the Plant Defensin NaD1 complexed with phosphatidic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-20-mer

Ligands

14 x PA8: 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PA8.1: 12 residues within 4Å: Chain A: S.36, K.37, I.38, L.39, R.40, R.41 Chain B: K.5, H.34, K.37, L.43 Chain D: K.37 Ligands: PA8.2 14 PLIP interactions: 9 interactions with chain A, 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: A:S.36, A:S.36, A:S.36, A:K.37, A:I.38, A:L.39, A:R.40 Water bridges: A:R.41, D:K.37 Salt bridges: A:R.41, D:K.37 Hydrophobic interactions: B:K.37, B:K.37, B:L.43 PA8.2: 11 residues within 4Å: Chain B: S.36, K.37, I.38, L.39, R.41 Chain D: K.37, I.38, R.40 Ligands: PA8.1, PA8.4, PA8.5 11 PLIP interactions: 4 interactions with chain D, 7 interactions with chain B Water bridges: D:R.40 Salt bridges: D:K.37, D:K.37, D:R.40, B:R.41 Hydrogen bonds: B:S.36, B:S.36, B:S.36, B:K.37, B:I.38, B:L.39 PA8.4: 12 residues within 4Å: Chain A: K.37, I.38, L.39, R.40 Chain C: S.36, I.38, L.39, R.40, R.41 Ligands: PA8.2, PA8.5, PA8.6 11 PLIP interactions: 3 interactions with chain A, 7 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: A:I.38, A:L.39 Salt bridges: A:R.40, C:R.41 Hydrogen bonds: C:S.36, C:K.37, C:I.38, C:L.39, C:R.40 Water bridges: C:R.41, F:K.37 PA8.5: 11 residues within 4Å: Chain A: I.38 Chain D: S.36, K.37, I.38, L.39, R.41 Chain F: K.37, I.38 Chain M: I.14 Ligands: PA8.2, PA8.4 13 PLIP interactions: 7 interactions with chain D, 6 interactions with chain F Hydrogen bonds: D:S.36, D:S.36, D:I.38, D:L.39, D:R.40 Water bridges: D:K.37, F:K.37, F:K.37, F:K.37, F:R.40 Salt bridges: D:R.41, F:K.37, F:R.40 PA8.6: 11 residues within 4Å: Chain C: I.14, K.37, I.38, R.40 Chain E: S.36, K.37, I.38, L.39, R.41 Chain F: I.38 Ligands: PA8.4 8 PLIP interactions: 5 interactions with chain E, 2 interactions with chain C, 1 interactions with chain F Hydrogen bonds: E:S.36, E:K.37, E:I.38, E:L.39 Salt bridges: E:R.41 Hydrophobic interactions: C:I.14, C:R.40, F:I.38 PA8.11: 8 residues within 4Å: Chain H: S.36, K.37, I.38, L.39, R.40, R.41 Chain J: K.37 Ligands: EDO.17 11 PLIP interactions: 9 interactions with chain H, 2 interactions with chain J Hydrophobic interactions: H:I.38 Hydrogen bonds: H:S.36, H:S.36, H:I.38, H:L.39, H:R.40 Water bridges: H:K.37, H:R.41, J:K.37 Salt bridges: H:R.41, J:K.37 PA8.12: 11 residues within 4Å: Chain G: K.37, I.38, R.40 Chain I: S.36, K.37, I.38, L.39, R.41 Chain J: I.38 Ligands: EDO.10, PGE.15 11 PLIP interactions: 6 interactions with chain I, 4 interactions with chain G, 1 interactions with chain J Hydrogen bonds: I:I.38, I:L.39, I:R.40 Water bridges: I:K.37, I:R.41, G:K.37 Salt bridges: I:R.41, G:K.37, G:R.40 Hydrophobic interactions: G:I.38, J:I.38 PA8.16: 12 residues within 4Å: Chain I: K.37 Chain K: I.38, L.39 Chain L: S.36, K.37, I.38, L.39, R.40, R.41 Chain N: K.37, I.38, R.40 18 PLIP interactions: 1 interactions with chain K, 6 interactions with chain N, 9 interactions with chain L, 2 interactions with chain I Hydrophobic interactions: K:L.39, L:I.38, I:K.37, I:K.37 Water bridges: N:K.37, N:R.40, N:R.40, L:K.37 Salt bridges: N:K.37, N:K.37, N:R.40, L:R.41 Hydrogen bonds: L:S.36, L:S.36, L:S.36, L:I.38, L:L.39, L:R.40 PA8.18: 12 residues within 4Å: Chain K: K.37, I.38, R.40 Chain M: S.36, K.37, I.38, L.39, R.40, R.41 Chain N: I.38, L.39 Ligands: PGE.14 14 PLIP interactions: 6 interactions with chain M, 5 interactions with chain K, 3 interactions with chain N Hydrogen bonds: M:S.36, M:S.36, M:I.38, M:L.39, M:R.40 Salt bridges: M:R.41, K:K.37 Hydrophobic interactions: K:R.40, N:I.38, N:I.38, N:L.39 Water bridges: K:K.37, K:K.37, K:R.40 PA8.21: 10 residues within 4Å: Chain H: I.16 Chain O: I.38 Chain P: S.36, K.37, I.38, L.39, R.41 Chain R: K.37, I.38, R.40 7 PLIP interactions: 4 interactions with chain P, 1 interactions with chain R, 1 interactions with chain O, 1 interactions with chain H Hydrogen bonds: P:S.36, P:I.38, P:L.39 Salt bridges: P:R.41 Water bridges: R:R.40 Hydrophobic interactions: O:I.38, H:I.16 PA8.22: 13 residues within 4Å: Chain H: I.14, R.40 Chain J: I.16 Chain O: K.37, I.38, R.40 Chain Q: S.36, K.37, I.38, L.39, R.40, R.41 Ligands: PA8.24 14 PLIP interactions: 9 interactions with chain Q, 1 interactions with chain H, 2 interactions with chain T, 1 interactions with chain O, 1 interactions with chain J Hydrophobic interactions: Q:L.39, H:R.40, O:I.38, J:I.16 Hydrogen bonds: Q:S.36, Q:S.36, Q:I.38, Q:L.39, Q:R.40 Water bridges: Q:K.37, Q:R.41, T:K.37, T:K.37 Salt bridges: Q:R.41 PA8.24: 13 residues within 4Å: Chain O: K.37 Chain Q: I.38 Chain R: S.36, K.37, I.38, L.39, R.40, R.41 Chain T: K.37, I.38, R.40 Ligands: PA8.22, PA8.25 15 PLIP interactions: 9 interactions with chain R, 3 interactions with chain T, 1 interactions with chain Q, 2 interactions with chain O Hydrophobic interactions: R:I.38, T:I.38, Q:I.38 Hydrogen bonds: R:S.36, R:S.36, R:S.36, R:I.38, R:L.39, R:R.40 Water bridges: R:R.41, T:R.40, O:K.37 Salt bridges: R:R.41, T:R.40, O:K.37 PA8.25: 10 residues within 4Å: Chain J: I.16 Chain Q: K.37, I.38 Chain S: S.36, K.37, I.38, L.39, R.41 Ligands: PA8.24, PA8.26 15 PLIP interactions: 9 interactions with chain S, 5 interactions with chain Q, 1 interactions with chain J Hydrogen bonds: S:S.36, S:S.36, S:S.36, S:I.38, S:L.39, S:R.40 Water bridges: S:K.37, S:R.41, Q:R.40, Q:R.40 Salt bridges: S:R.41, Q:R.40 Hydrophobic interactions: Q:I.38, Q:I.38, J:I.16 PA8.26: 6 residues within 4Å: Chain T: S.36, I.38, L.39, R.40, R.41 Ligands: PA8.25 7 PLIP interactions: 7 interactions with chain T Hydrogen bonds: T:S.36, T:S.36, T:I.38, T:L.39, T:R.40 Water bridges: T:K.37 Salt bridges: T:R.41

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

PO4.3: 2 residues within 4Å: Chain B: K.37, R.40 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.40 PO4.8: 5 residues within 4Å: Chain G: S.36, K.37, I.38, L.39 Chain J: K.37 9 PLIP interactions: 6 interactions with chain G, 3 interactions with chain J Hydrogen bonds: G:S.36, G:S.36, G:K.37, G:I.38, G:L.39, G:R.40 Water bridges: J:K.37, J:K.37 Salt bridges: J:K.37 PO4.9: 1 residues within 4Å: Chain G: R.41 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:R.41

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 9 residues within 4Å: Chain C: K.18, P.19, R.22 Chain E: T.6, E.7, S.8, N.9 Chain F: R.2, E.3 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:T.6, F:E.3 Water bridges: E:E.7 PGE.13: 4 residues within 4Å: Chain B: I.38 Chain I: I.38, R.40 Ligands: PGE.14 No protein-ligand interaction detected (PLIP) PGE.14: 6 residues within 4Å: Chain B: L.39 Chain I: R.40 Chain K: I.14, I.38 Ligands: PGE.13, PA8.18 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.40 PGE.15: 5 residues within 4Å: Chain I: I.38 Chain J: I.38, L.39 Chain L: K.37 Ligands: PA8.12 No protein-ligand interaction detected (PLIP) PGE.19: 7 residues within 4Å: Chain D: I.38, L.39 Chain K: I.14, I.16 Chain M: I.38, L.39, R.40 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:I.38

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

EDO.10: 2 residues within 4Å: Chain G: L.39 Ligands: PA8.12 No protein-ligand interaction detected (PLIP) EDO.17: 4 residues within 4Å: Chain J: I.38, L.39 Chain L: R.40 Ligands: PA8.11 No protein-ligand interaction detected (PLIP) EDO.20: 4 residues within 4Å: Chain O: E.3, T.31, K.46, P.47 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:E.3, O:T.31 EDO.23: 3 residues within 4Å: Chain Q: R.22, K.23, I.26 No protein-ligand interaction detected (PLIP) EDO.27: 7 residues within 4Å: Chain T: A.1, R.2, E.3, T.31, T.45, K.46, P.47 3 PLIP interactions: 3 interactions with chain T Hydrogen bonds: T:A.1, T:T.31, T:T.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jarva, M. et al., X-ray structure of a carpet-like antimicrobial defensin-phospholipid membrane disruption complex. Nat Commun (2018)

Release Date

2018-05-23

Peptides

Flower-specific defensin: ABCDEFGHIJKLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

Flower-specific defensin