SMTL ID : 8qyh.1

Zorya anti-bacteriophage defense system ZorAB ZorA E86A_E89A, Calcium binding site mutation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-2-mer

Ligands

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 21 residues within 4Å: Chain A: F.31, L.39, I.46, I.192, L.193, W.196, L.197, L.200, S.201, K.204, K.207, Y.208 Chain E: T.26, F.29, A.30, C.33, F.37, R.41, N.128, F.131 Ligands: PEE.10 24 PLIP interactions: 17 interactions with chain A, 7 interactions with chain E Hydrophobic interactions: A:F.31, A:L.39, A:I.192, A:L.193, A:W.196, A:W.196, A:W.196, A:L.197, A:L.197, A:K.204, E:T.26, E:F.29, E:A.30, E:F.37, E:F.37, E:F.131 Hydrogen bonds: A:Y.208, A:Y.208 Salt bridges: A:K.50, A:K.204, A:K.204, A:K.204, A:K.207, E:R.41 CDL.3: 21 residues within 4Å: Chain A: F.29, A.30, C.33, F.37, R.41, N.128, F.131, F.132, I.138 Chain B: F.31, L.39, F.189, I.192, L.193, W.196, L.197, L.200, S.201, K.204, K.207 Ligands: PEE.2 23 PLIP interactions: 15 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.31, B:L.39, B:F.189, B:F.189, B:L.193, B:L.193, B:W.196, B:W.196, B:W.196, B:W.196, B:L.200, B:K.204, A:F.29, A:F.29, A:A.30, A:F.131, A:F.131, A:F.132, A:I.138 Salt bridges: B:K.204, B:K.204, B:K.207 Hydrogen bonds: A:R.41 CDL.5: 22 residues within 4Å: Chain B: T.26, F.29, A.30, F.37, R.41, N.128, F.131, F.132, L.135 Chain C: L.39, I.46, K.50, F.189, I.192, L.193, W.196, L.197, L.200, S.201, K.204, Y.208 Ligands: PEE.4 26 PLIP interactions: 11 interactions with chain B, 15 interactions with chain C Hydrophobic interactions: B:T.26, B:F.29, B:F.29, B:A.30, B:F.37, B:F.132, B:L.135, C:L.39, C:I.46, C:F.189, C:I.192, C:L.193, C:W.196, C:W.196, C:L.197, C:L.197, C:L.200 Hydrogen bonds: B:N.128 Water bridges: B:P.126, B:N.128 Salt bridges: B:R.41, C:K.50, C:K.204, C:K.204, C:K.204, C:K.204 CDL.7: 18 residues within 4Å: Chain C: T.26, F.29, A.30, C.33, F.37, R.41, N.128, F.131, F.132 Chain D: K.50, F.189, W.196, L.197, L.200, S.201, K.204, K.207, Y.208 25 PLIP interactions: 12 interactions with chain C, 13 interactions with chain D Hydrophobic interactions: C:F.29, C:F.29, C:F.29, C:A.30, C:F.37, C:F.37, C:F.131, C:F.131, C:F.132, D:F.189, D:W.196, D:W.196, D:L.197, D:L.200, D:L.200, D:K.204 Hydrogen bonds: C:N.128, D:Y.208 Water bridges: C:N.128 Salt bridges: C:R.41, D:K.50, D:K.204, D:K.204, D:K.207, D:K.207 CDL.9: 21 residues within 4Å: Chain D: T.26, F.29, C.33, F.37, R.41, N.128, F.131, F.132, M.142 Chain E: I.43, I.46, F.189, I.192, L.193, W.196, L.197, L.200, S.201, K.204, K.207, Y.208 20 PLIP interactions: 6 interactions with chain D, 14 interactions with chain E Hydrophobic interactions: D:F.29, D:F.29, D:F.132, E:F.189, E:L.193, E:L.193, E:W.196, E:W.196, E:W.196, E:W.196, E:L.197, E:K.204 Hydrogen bonds: D:N.128, E:Y.208 Water bridges: D:F.131 Salt bridges: D:R.41, E:K.204, E:K.204, E:K.204, E:K.207

5 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.2: 18 residues within 4Å: Chain A: I.7, L.11, S.13, V.14, K.18, V.19, T.22, V.23, T.26, M.142, I.145, Y.149 Chain B: I.24, L.182, A.185, F.186, F.189 Ligands: CDL.3 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.7, A:L.11, A:L.11, A:K.18, A:V.19, A:V.23, A:T.26, A:M.142, A:I.145, A:Y.149, B:I.24, B:L.182, B:F.186, B:F.186, B:F.189, B:F.189 Salt bridges: A:K.18 PEE.4: 16 residues within 4Å: Chain B: I.7, T.10, L.11, S.13, V.14, E.15, T.22, T.26, M.142, I.145, G.146, Y.149 Chain C: L.182, F.186, F.189 Ligands: CDL.5 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:I.7, B:L.11, B:V.14, B:T.26, C:L.182, C:F.186, C:F.189, C:F.189 Hydrogen bonds: B:S.13 Water bridges: B:K.18 Salt bridges: B:K.18 PEE.6: 17 residues within 4Å: Chain C: T.10, L.11, S.13, V.14, E.15, K.18, V.19, T.22, V.23, M.142, I.145, G.146, Y.149 Chain D: L.182, A.185, F.186, F.189 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:L.11, C:L.11, C:V.14, C:V.14, C:T.22, C:V.23, C:Y.149, C:Y.149, D:L.182, D:A.185, D:F.186, D:F.189, D:F.189 Hydrogen bonds: C:S.13, C:E.15 Salt bridges: C:K.18, C:K.18 PEE.8: 18 residues within 4Å: Chain D: L.11, S.13, V.14, E.15, K.18, V.19, T.22, V.23, T.26, M.142, I.145, G.146, Y.149 Chain E: L.178, F.181, L.182, A.185, F.189 22 PLIP interactions: 16 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:L.11, D:L.11, D:L.11, D:V.14, D:V.14, D:K.18, D:V.19, D:V.19, D:T.22, D:V.23, D:M.142, D:I.145, D:Y.149, D:Y.149, E:F.181, E:F.181, E:L.182, E:A.185, E:F.189, E:F.189 Hydrogen bonds: D:E.15 Salt bridges: D:K.18 PEE.10: 16 residues within 4Å: Chain A: F.186, F.189 Chain E: T.10, L.11, S.13, V.14, E.15, K.18, T.22, V.23, T.26, M.142, I.145, G.146, Y.149 Ligands: CDL.1 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:T.10, E:L.11, E:V.14, E:T.26, E:M.142, E:Y.149, E:Y.149 Hydrogen bonds: E:S.13 Salt bridges: E:K.18, E:K.18

Links

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Citation

Hu, H. et al., Structure and mechanism of the Zorya anti-phage defense system. Nature (2024)

Release Date

2024-11-06

Peptides

Anti-phage defense ZorAB system ZorA: ABCDE
Membrane protein: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Membrane

We predict this structure to be a membrane protein.
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Anti-phage defense ZorAB system ZorA

Membrane protein

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