SMTL ID : 5vyp.1

Crystal structure of the Plant Defensin NsD7 bound to PIP2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-24-mer

Ligands

24 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.1: 19 residues within 4Å: Chain A: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain B: R.41 Chain C: K.37, I.38 Chain T: K.37, I.38 Chain V: I.38 Ligands: PIO.4, PIO.7, PIO.40, PIO.44 17 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, 1 interactions with chain V Hydrophobic interactions: A:I.38, V:I.38 Hydrogen bonds: A:S.36, A:K.37, A:K.37, A:I.38, A:L.39, A:R.41 Water bridges: A:K.5 Salt bridges: A:K.2, A:K.2, A:K.5, A:K.5, A:H.34, A:K.37, A:R.41, B:R.41 PIO.4: 22 residues within 4Å: Chain A: I.38, R.41 Chain B: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain C: K.2, K.37 Chain R: I.16, R.40 Chain T: I.16, L.39, R.40 Chain V: L.39 Ligands: PIO.1, PIO.5, PIO.7 23 PLIP interactions: 3 interactions with chain T, 14 interactions with chain B, 2 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: T:I.16, T:I.16, T:R.40, B:I.38, A:I.38 Hydrogen bonds: B:K.37, B:I.38, B:L.39, B:R.41, A:R.41 Water bridges: B:K.2, B:K.37, A:K.5 Salt bridges: B:K.2, B:K.2, B:K.5, B:K.5, B:H.34, B:K.37, B:R.41, C:K.2, C:K.37, A:R.41 PIO.5: 19 residues within 4Å: Chain B: K.2, K.37 Chain C: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41 Chain D: I.38, R.41 Chain E: K.37, I.38 Ligands: PIO.4, PIO.7, PIO.10, PIO.34, PIO.44 18 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D, 3 interactions with chain B, 2 interactions with chain E Hydrogen bonds: C:K.37, C:I.38, C:L.39, C:R.40, C:R.41 Water bridges: C:K.37, B:K.2 Salt bridges: C:K.2, C:K.5, C:K.5, C:H.34, C:K.37, C:R.41, D:R.41, B:K.2, B:K.37, E:K.37 Hydrophobic interactions: E:I.38 PIO.7: 20 residues within 4Å: Chain B: K.37, I.38 Chain C: I.38, R.41 Chain D: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain E: K.2, K.37 Ligands: PIO.1, PIO.4, PIO.5, PIO.32, PIO.40 18 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C, 1 interactions with chain B, 2 interactions with chain E Hydrogen bonds: D:S.36, D:K.37, D:I.38, D:L.39, D:R.41 Water bridges: D:K.37, D:K.37 Salt bridges: D:K.2, D:K.2, D:K.5, D:H.34, D:K.37, D:R.41, C:R.41, E:K.2, E:K.37 Hydrophobic interactions: C:I.38, B:I.38 PIO.9: 16 residues within 4Å: Chain D: K.2, K.37 Chain E: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41 Chain F: R.41 Chain G: K.37, I.38 Ligands: PIO.10, PIO.34, GOL.42 18 PLIP interactions: 12 interactions with chain E, 2 interactions with chain F, 1 interactions with chain G, 3 interactions with chain D Hydrophobic interactions: E:I.38 Hydrogen bonds: E:K.37, E:I.38, E:L.39, E:R.41, F:R.41 Water bridges: E:K.37, D:K.37 Salt bridges: E:K.2, E:K.2, E:K.5, E:H.34, E:K.37, E:R.41, F:R.41, G:K.37, D:K.2, D:K.37 PIO.10: 15 residues within 4Å: Chain D: K.37, I.38 Chain E: R.41 Chain F: K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain G: K.37 Ligands: PIO.5, PIO.9, PIO.11 14 PLIP interactions: 9 interactions with chain F, 2 interactions with chain D, 2 interactions with chain G, 1 interactions with chain E Hydrogen bonds: F:K.37, F:I.38, F:L.39, F:R.40, F:R.41 Salt bridges: F:K.5, F:K.5, F:H.34, F:R.41, D:K.37, G:K.37, G:K.37, E:R.41 Hydrophobic interactions: D:I.38 PIO.11: 18 residues within 4Å: Chain F: K.37 Chain G: K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain H: I.38, R.41 Chain I: K.37, I.38 Ligands: PIO.10, PIO.13, PIO.16, PIO.30, GOL.39 15 PLIP interactions: 10 interactions with chain G, 2 interactions with chain F, 1 interactions with chain I, 2 interactions with chain H Hydrophobic interactions: G:L.39, I:I.38, H:I.38 Hydrogen bonds: G:K.37, G:I.38, G:L.39, G:R.41 Salt bridges: G:K.5, G:K.5, G:H.34, G:K.37, G:R.41, F:K.37, H:R.41 Water bridges: F:K.37 PIO.13: 19 residues within 4Å: Chain F: K.37, I.38 Chain G: I.38, R.41 Chain H: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain I: K.2, K.37 Ligands: PIO.11, PIO.14, PIO.24, PIO.28 17 PLIP interactions: 13 interactions with chain H, 2 interactions with chain I, 2 interactions with chain G Hydrophobic interactions: H:L.39, G:I.38 Hydrogen bonds: H:K.37, H:I.38, H:L.39, H:R.40, H:R.41 Salt bridges: H:K.2, H:K.2, H:K.5, H:K.5, H:H.34, H:K.37, H:R.41, I:K.2, I:K.37, G:R.41 PIO.14: 20 residues within 4Å: Chain H: K.2, K.37 Chain I: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41 Chain J: I.38, R.41 Chain K: K.37, I.38 Ligands: PIO.13, PIO.16, PIO.17, PIO.18, PIO.23, PIO.26 18 PLIP interactions: 2 interactions with chain J, 2 interactions with chain K, 2 interactions with chain H, 12 interactions with chain I Hydrogen bonds: J:R.41, I:K.37, I:I.38, I:L.39, I:R.41 Salt bridges: J:R.41, K:K.37, H:K.2, H:K.37, I:K.2, I:K.2, I:K.5, I:K.5, I:H.34, I:K.37, I:R.41 Hydrophobic interactions: K:I.38, I:I.38 PIO.16: 20 residues within 4Å: Chain H: K.37 Chain I: I.38, R.41 Chain J: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain K: K.2, K.37 Ligands: PIO.11, PIO.14, PIO.17, PIO.19, PIO.23, PIO.24 17 PLIP interactions: 1 interactions with chain H, 11 interactions with chain J, 4 interactions with chain K, 1 interactions with chain I Salt bridges: H:K.37, J:K.2, J:K.5, J:K.5, J:H.34, J:K.37, J:R.41, K:K.2, K:K.37, I:R.41 Hydrogen bonds: J:S.36, J:K.37, J:I.38, J:L.39, J:R.41 Water bridges: K:K.37, K:K.37 PIO.17: 23 residues within 4Å: Chain J: K.37 Chain K: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain L: I.38, R.41 Chain O: L.39 Chain Q: I.14, I.38, L.39, R.40 Chain S: I.16, R.40 Ligands: PIO.14, PIO.16, PIO.18, GOL.27 21 PLIP interactions: 3 interactions with chain Q, 14 interactions with chain K, 1 interactions with chain S, 1 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: Q:I.14, Q:L.39, Q:R.40, K:I.38, S:I.16 Hydrogen bonds: K:K.37, K:I.38, K:L.39, K:R.41, J:K.37 Water bridges: K:K.37, K:K.37 Salt bridges: K:K.2, K:K.2, K:K.5, K:K.5, K:H.34, K:K.37, K:R.41, L:R.41, J:K.37 PIO.18: 15 residues within 4Å: Chain J: K.37 Chain K: R.41 Chain L: K.5, H.34, S.36, K.37, I.38, L.39, R.41 Chain Q: K.37, I.38, R.40 Ligands: PIO.14, PIO.17, PIO.19 14 PLIP interactions: 11 interactions with chain L, 1 interactions with chain J, 2 interactions with chain K Hydrogen bonds: L:S.36, L:S.36, L:K.37, L:I.38, L:L.39, L:R.41, K:R.41 Salt bridges: L:K.5, L:K.5, L:H.34, L:K.37, L:R.41, J:K.37, K:R.41 PIO.19: 16 residues within 4Å: Chain J: I.38 Chain M: K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain N: R.41 Chain O: K.37, I.38 Ligands: PIO.16, PIO.18, PIO.22, PIO.24 16 PLIP interactions: 4 interactions with chain O, 10 interactions with chain M, 1 interactions with chain N, 1 interactions with chain J Hydrophobic interactions: O:I.38, O:I.38, O:I.38, M:L.39, J:I.38 Salt bridges: O:K.37, M:K.5, M:K.5, M:H.34, M:R.41, N:R.41 Hydrogen bonds: M:S.36, M:K.37, M:I.38, M:L.39, M:R.41 PIO.22: 23 residues within 4Å: Chain F: I.16, R.40 Chain H: I.14, I.16, L.39, R.40 Chain J: L.39 Chain M: I.38, R.41 Chain N: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain O: K.2, K.37 Ligands: PIO.19, PIO.23, PIO.24 20 PLIP interactions: 1 interactions with chain F, 13 interactions with chain N, 2 interactions with chain O, 3 interactions with chain M, 1 interactions with chain H Hydrophobic interactions: F:I.16, M:I.38, H:I.16 Hydrogen bonds: N:K.37, N:I.38, N:L.39, N:R.41, M:R.41 Water bridges: N:K.37, N:K.37 Salt bridges: N:K.2, N:K.2, N:K.5, N:K.5, N:H.34, N:K.37, N:R.41, O:K.2, O:K.37, M:R.41 PIO.23: 20 residues within 4Å: Chain N: K.2, K.37 Chain O: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain P: I.38, R.41 Chain Q: K.37, I.38 Ligands: PIO.14, PIO.16, PIO.22, PIO.24, PIO.28 21 PLIP interactions: 12 interactions with chain O, 4 interactions with chain N, 3 interactions with chain Q, 2 interactions with chain P Hydrogen bonds: O:K.37, O:I.38, O:L.39, O:R.40, O:R.41, P:R.41 Salt bridges: O:K.2, O:K.2, O:K.5, O:K.5, O:H.34, O:K.37, O:R.41, N:K.2, N:K.37, Q:K.37, P:R.41 Water bridges: N:K.37, N:K.37 Hydrophobic interactions: Q:I.38, Q:I.38 PIO.24: 20 residues within 4Å: Chain N: K.37, I.38 Chain O: I.38, R.41 Chain P: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain Q: K.2, K.37 Ligands: PIO.13, PIO.16, PIO.19, PIO.22, PIO.23 20 PLIP interactions: 2 interactions with chain N, 2 interactions with chain Q, 13 interactions with chain P, 3 interactions with chain O Hydrophobic interactions: N:I.38, O:I.38 Salt bridges: N:K.37, Q:K.2, Q:K.37, P:K.2, P:K.2, P:K.5, P:K.5, P:H.34, P:K.37, P:R.41, O:R.41 Hydrogen bonds: P:K.37, P:I.38, P:L.39, P:R.41, O:R.41 Water bridges: P:K.37, P:K.37 PIO.26: 17 residues within 4Å: Chain P: K.2, K.37 Chain Q: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41 Chain R: I.38, R.41 Chain S: K.37, I.38 Ligands: PIO.14, PIO.28, PIO.32 20 PLIP interactions: 11 interactions with chain Q, 3 interactions with chain P, 3 interactions with chain R, 3 interactions with chain S Hydrogen bonds: Q:K.37, Q:I.38, Q:L.39, Q:R.41, R:R.41 Salt bridges: Q:K.2, Q:K.2, Q:K.5, Q:K.5, Q:H.34, Q:K.37, Q:R.41, P:K.2, P:K.37, R:R.41, S:K.37 Water bridges: P:K.37 Hydrophobic interactions: R:I.38, S:K.37, S:I.38 PIO.28: 18 residues within 4Å: Chain P: K.37, I.38 Chain Q: I.38, R.41 Chain R: K.5, H.34, S.36, K.37, I.38, L.39, R.40, R.41, L.43 Chain S: K.37 Ligands: PIO.13, PIO.23, PIO.26, PIO.30 15 PLIP interactions: 10 interactions with chain R, 3 interactions with chain Q, 1 interactions with chain S, 1 interactions with chain P Hydrophobic interactions: R:I.38, Q:I.38, P:I.38 Hydrogen bonds: R:K.37, R:I.38, R:L.39, R:R.40, R:R.41 Salt bridges: R:K.5, R:K.5, R:H.34, R:R.41, Q:K.5, Q:R.41, S:K.37 PIO.30: 16 residues within 4Å: Chain R: K.37 Chain S: K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain T: I.38, R.41 Chain U: K.37 Ligands: PIO.11, PIO.28, PIO.32, PIO.40 15 PLIP interactions: 11 interactions with chain S, 2 interactions with chain T, 1 interactions with chain R, 1 interactions with chain U Hydrophobic interactions: S:I.38, T:I.38 Hydrogen bonds: S:K.37, S:I.38, S:L.39, S:R.40, S:R.41 Salt bridges: S:K.2, S:K.5, S:K.5, S:H.34, S:R.41, T:R.41, R:K.37, U:K.37 PIO.32: 18 residues within 4Å: Chain R: K.37, I.38 Chain S: I.38, R.41 Chain T: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41 Chain U: K.2, K.37 Ligands: PIO.7, PIO.26, SO4.29, PIO.30 19 PLIP interactions: 3 interactions with chain S, 14 interactions with chain T, 2 interactions with chain U Hydrophobic interactions: S:I.38, T:L.39 Hydrogen bonds: S:R.41, T:K.37, T:I.38, T:L.39, T:R.41 Salt bridges: S:R.41, T:K.2, T:K.2, T:K.5, T:K.5, T:H.34, T:K.37, T:R.41, U:K.2, U:K.37 Water bridges: T:K.37, T:K.37 PIO.34: 18 residues within 4Å: Chain T: K.37 Chain U: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain V: I.38, R.41 Chain W: I.38 Ligands: PIO.5, PIO.9, PIO.40, PIO.41, PIO.44 20 PLIP interactions: 2 interactions with chain V, 15 interactions with chain U, 2 interactions with chain W, 1 interactions with chain T Hydrophobic interactions: V:I.38, U:I.38, W:I.38 Salt bridges: V:R.41, U:K.2, U:K.2, U:K.5, U:K.5, U:H.34, U:K.37, U:R.41, W:K.37, T:K.37 Hydrogen bonds: U:K.37, U:I.38, U:L.39, U:R.40, U:R.41 Water bridges: U:K.2, U:K.37 PIO.40: 18 residues within 4Å: Chain T: K.37, I.38 Chain U: I.38, R.41 Chain V: K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain W: K.37 Ligands: PIO.1, PIO.7, PIO.30, PIO.34, PIO.41 16 PLIP interactions: 11 interactions with chain V, 2 interactions with chain W, 1 interactions with chain U, 2 interactions with chain T Hydrophobic interactions: V:I.38, T:I.38 Hydrogen bonds: V:S.36, V:K.37, V:I.38, V:L.39, V:R.41, W:K.37 Salt bridges: V:K.5, V:K.5, V:H.34, V:K.37, V:R.41, W:K.37, U:R.41, T:K.37 PIO.41: 23 residues within 4Å: Chain C: I.38, L.39 Chain E: I.14, I.16, I.38, L.39 Chain G: R.40 Chain V: K.37 Chain W: K.2, K.5, H.34, S.36, K.37, I.38, L.39, R.41, L.43 Chain X: I.38, R.41 Ligands: PIO.34, PIO.40, GOL.42, PIO.44 17 PLIP interactions: 12 interactions with chain W, 2 interactions with chain X, 2 interactions with chain V, 1 interactions with chain E Hydrophobic interactions: W:I.38, X:I.38, E:I.14 Hydrogen bonds: W:S.36, W:K.37, W:I.38, W:L.39, W:R.41 Salt bridges: W:K.2, W:K.5, W:K.5, W:H.34, W:K.37, W:R.41, X:R.41, V:K.37, V:K.37 PIO.44: 16 residues within 4Å: Chain E: K.37, I.38 Chain V: K.37 Chain W: R.41 Chain X: K.5, H.34, S.36, K.37, I.38, L.39, R.41 Ligands: PIO.1, PIO.5, PIO.34, PIO.41, GOL.43 12 PLIP interactions: 1 interactions with chain W, 10 interactions with chain X, 1 interactions with chain V Salt bridges: W:R.41, X:K.5, X:K.5, X:H.34, X:K.37, X:R.41, V:K.37 Hydrophobic interactions: X:L.39 Hydrogen bonds: X:K.37, X:I.38, X:L.39, X:R.41

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

SO4.2: 2 residues within 4Å: Chain A: P.19, K.23 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.23 SO4.3: 1 residues within 4Å: Chain A: P.20 No protein-ligand interaction detected (PLIP) SO4.8: 3 residues within 4Å: Chain D: L.39 Chain R: I.14 Ligands: SO4.29 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Salt bridges: B:R.40 Hydrogen bonds: D:L.39 SO4.12: 4 residues within 4Å: Chain G: I.14, L.39 Ligands: SO4.35, GOL.42 1 PLIP interactions: 1 interactions with chain I Salt bridges: I:R.40 SO4.29: 4 residues within 4Å: Chain R: I.38, L.39 Ligands: SO4.8, PIO.32 No protein-ligand interaction detected (PLIP) SO4.35: 5 residues within 4Å: Chain U: I.14, I.38, L.39, R.40 Ligands: SO4.12 No protein-ligand interaction detected (PLIP) SO4.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.37: 3 residues within 4Å: Chain U: K.23, R.27 Ligands: GOL.38 1 PLIP interactions: 1 interactions with chain U Salt bridges: U:K.23

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: L.39, R.41 Chain C: I.16, C.35, R.40 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:C.35, C:R.40, C:R.40, A:L.39 Water bridges: A:R.41 GOL.15: 2 residues within 4Å: Chain I: L.39 Ligands: GOL.31 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:L.39 GOL.20: 2 residues within 4Å: Chain M: C.48 Chain N: K.29 No protein-ligand interaction detected (PLIP) GOL.21: 4 residues within 4Å: Chain M: T.17, P.19, P.20, K.23 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:K.23, M:K.23 GOL.25: 3 residues within 4Å: Chain N: R.40 Chain P: I.14, L.39 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:R.40 GOL.27: 6 residues within 4Å: Chain O: I.14, L.39, R.41 Chain Q: I.16, R.40 Ligands: PIO.17 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:R.40, Q:R.40 GOL.31: 6 residues within 4Å: Chain S: I.14, I.38, L.39 Chain U: I.16 Ligands: GOL.15, GOL.39 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:I.38 GOL.33: 10 residues within 4Å: Chain T: I.16, T.17, K.18, R.40 Chain V: F.11, P.12, G.13, I.14, L.39, R.41 5 PLIP interactions: 3 interactions with chain T, 2 interactions with chain V Hydrogen bonds: T:I.16, T:K.18, T:R.40, V:F.11, V:L.39 GOL.38: 2 residues within 4Å: Chain U: K.23 Ligands: SO4.37 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:K.23 GOL.39: 6 residues within 4Å: Chain S: L.39 Chain U: K.37, I.38, R.40 Ligands: PIO.11, GOL.31 No protein-ligand interaction detected (PLIP) GOL.42: 6 residues within 4Å: Chain G: R.40 Chain W: K.37, I.38 Ligands: PIO.9, SO4.12, PIO.41 No protein-ligand interaction detected (PLIP) GOL.43: 5 residues within 4Å: Chain E: G.13, I.14 Chain W: L.39, R.41 Ligands: PIO.44 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jarva, M. et al., Structure of the defensin NsD7 in complex with PIP2 reveals that defensin : lipid oligomer topologies are dependent on lipid type. FEBS Lett. (2017)

Release Date

2017-08-02

Peptides

Defensin NsD7: ABCDEFGHIJKLMNOPQRSTUVWX

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

U
U

V
V

W
W

X
X

Defensin NsD7

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