SMTL ID : 8qyd.1

Zorya anti-bacteriophage defense system ZorAB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-2-mer

Ligands

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 20 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, C.33, F.37, R.41, N.128, F.131 Ligands: PEE.15 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:F.31, A:L.39, A:I.46, A:I.192, A:L.193, A:W.196, A:W.196, A:W.196, A:L.197, A:L.197, A:L.200, A:K.204, E:T.26, E:F.29, E:F.29, E:F.37, E:F.37 Hydrogen bonds: A:Y.208, A:Y.208 Salt bridges: A:K.204, A:K.204, A:K.204, A:K.207, E:R.41 CDL.4: 21 residues within 4Å: Chain A: T.26, F.29, A.30, C.33, F.37, R.41, N.128, F.131, F.132, I.138 Chain B: Y.47, F.189, I.192, L.193, W.196, L.197, L.200, S.201, K.204, K.207 Ligands: PEE.3 28 PLIP interactions: 16 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:F.189, B:I.192, B:L.193, B:L.193, B:L.193, B:W.196, B:W.196, B:W.196, B:W.196, B:L.197, B:L.200, A:T.26, A:F.29, A:F.29, A:A.30, A:F.37, A:F.131, A:F.131, A:F.132, A:F.132, A:I.138 Hydrogen bonds: B:Y.47, A:N.128 Salt bridges: B:K.50, B:K.204, B:K.204, B:K.207, A:R.41 CDL.7: 23 residues within 4Å: Chain B: V.25, T.26, F.29, A.30, F.37, R.41, N.128, F.131, F.132 Chain C: L.39, I.46, K.50, F.189, I.192, L.193, W.196, L.197, L.200, S.201, K.204, K.207, Y.208 Ligands: PEE.5 26 PLIP interactions: 16 interactions with chain C, 10 interactions with chain B Hydrophobic interactions: 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.200, B:V.25, B:T.26, B:F.29, B:F.29, B:F.29, B:A.30, B:F.37, B:F.132 Hydrogen bonds: C:Y.208, B:N.128 Salt bridges: C:K.50, C:K.204, C:K.204, C:K.204, C:K.204, C:K.207, B:R.41 CDL.10: 18 residues within 4Å: Chain C: T.26, F.29, F.37, R.41, N.128, F.131, F.132 Chain D: I.43, I.46, K.50, L.193, W.196, L.197, L.200, K.204, K.207, Y.208 Ligands: PEE.8 20 PLIP interactions: 8 interactions with chain C, 12 interactions with chain D Hydrophobic interactions: C:T.26, C:F.29, C:F.29, C:F.131, C:F.131, C:F.132, D:I.43, D:I.46, D:L.193, D:W.196, D:L.197 Hydrogen bonds: C:N.128, D:Y.208 Salt bridges: C:R.41, D:K.50, D:K.204, D:K.204, D:K.204, D:K.207, D:K.207 CDL.14: 21 residues within 4Å: Chain D: T.26, F.29, A.30, C.33, F.37, R.41, N.128, F.131, F.132, M.142 Chain E: I.43, F.189, I.192, L.193, W.196, L.197, L.200, S.201, K.204, K.207, Y.208 24 PLIP interactions: 14 interactions with chain E, 10 interactions with chain D Hydrophobic interactions: E:F.189, E:L.193, E:W.196, E:W.196, E:W.196, E:W.196, E:W.196, E:L.197, D:T.26, D:F.29, D:F.29, D:F.29, D:A.30, D:F.131, D:F.132 Hydrogen bonds: E:Y.208, D:N.128 Water bridges: E:K.204, D:R.41 Salt bridges: E:K.204, E:K.204, E:K.204, E:K.207, D:R.41

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.86, E.89 Chain B: D.217, Y.220 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.217, B:Y.220, A:E.86, A:E.89, H2O.3 CA.6: 4 residues within 4Å: Chain B: E.86, E.89 Chain C: D.217, Y.220 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.86, B:E.89, C:D.217, C:Y.220, H2O.4 CA.9: 4 residues within 4Å: Chain C: E.86, E.89 Chain D: D.217, Y.220 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:D.217, D:Y.220, C:E.89, H2O.8, H2O.8 CA.13: 4 residues within 4Å: Chain D: E.86, E.89 Chain E: D.217, Y.220 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: E:D.217, E:Y.220, D:E.89, H2O.8, H2O.8 CA.16: 4 residues within 4Å: Chain A: D.217, Y.220 Chain E: E.86, E.89 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: E:E.86, E:E.86, E:E.89, A:D.217, H2O.1

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

PEE.3: 16 residues within 4Å: Chain A: I.7, T.10, L.11, S.13, K.18, V.19, T.22, V.23, T.26, M.142, I.145, Y.149 Chain B: L.182, F.186, F.189 Ligands: CDL.4 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.7, A:T.10, A:L.11, A:K.18, A:V.19, A:V.23, A:T.26, A:I.145, A:Y.149, B:L.182, B:F.186, B:F.189, B:F.189 Hydrogen bonds: A:S.13 Salt bridges: A:K.18 PEE.5: 16 residues within 4Å: Chain B: I.7, T.10, V.14, E.15, K.18, V.19, T.22, V.23, M.142, I.145, G.146, Y.149 Chain C: I.24, F.186, F.189 Ligands: CDL.7 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:I.24, C:F.186, C:F.189, B:I.7, B:V.14, B:V.19, B:V.23, B:Y.149 Hydrogen bonds: B:S.13 Salt bridges: B:K.18 PEE.8: 16 residues within 4Å: Chain C: T.10, L.11, V.14, K.18, V.19, T.22, V.23, T.26, M.142, I.145, Y.149 Chain D: L.182, A.185, F.186, F.189 Ligands: CDL.10 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.11, C:L.11, C:V.19, C:T.22, C:V.23, C:T.26, C:M.142, C:I.145, C:Y.149, C:Y.149, D:L.182, D:F.189, D:F.189 Hydrogen bonds: C:E.15 Salt bridges: C:K.18 PEE.11: 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 21 PLIP interactions: 8 interactions with chain E, 13 interactions with chain D Hydrophobic interactions: E:L.178, E:F.181, E:F.181, E:L.182, E:A.185, E:F.189, E:F.189, E:F.189, D:L.11, D:V.14, D:K.18, D:K.18, D:V.19, D:V.23, D:M.142, D:I.145, D:Y.149, D:Y.149 Hydrogen bonds: D:E.15 Salt bridges: D:K.18, D:K.18 PEE.15: 17 residues within 4Å: Chain A: I.24, L.182, F.186, F.189 Chain E: I.7, T.10, L.11, S.13, V.14, E.15, K.18, V.19, T.22, V.23, I.145, Y.149 Ligands: CDL.1 15 PLIP interactions: 9 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: E:I.7, E:L.11, E:L.11, E:V.14, E:V.19, E:V.23, E:I.145, E:Y.149, A:I.24, A:L.182, A:F.186, A:F.186, A:F.189, A:F.189 Salt bridges: E:K.18

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.12: 16 residues within 4Å: Chain A: L.250, L.254, L.258 Chain B: L.250, L.254 Chain C: L.250, L.254, L.258, L.261 Chain D: L.250, L.254, L.258, L.261 Chain E: L.250, L.254, L.258 10 PLIP interactions: 2 interactions with chain C, 3 interactions with chain E, 1 interactions with chain B, 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: C:L.254, C:L.258, E:L.250, E:L.254, E:L.258, B:L.250, D:L.250, D:L.254, D:L.261, A:L.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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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