SMTL ID : 6eph.2 (3 other biounits)

Structure of the epsilon_1 / zeta_1 antitoxin toxin system from Neisseria gonorrhoeae in complex with UNAM.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x EPZ: (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid(Non-covalent)

EPZ.1: 21 residues within 4Å: Chain B: S.6, D.7, I.8, N.9, A.55, D.56, K.59, N.75, H.79, N.80, A.83, V.84, S.87, K.115, F.132, G.134, Q.135, S.141, R.144, K.145, I.187 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Q.135, B:I.187 Hydrogen bonds: B:S.6, B:D.7, B:N.9, B:N.75, B:H.79, B:A.83, B:S.87, B:Q.135, B:Q.135, B:S.141, B:R.144, B:K.145 Water bridges: B:K.59, B:S.86, B:S.87, B:R.144 Salt bridges: B:K.59, B:H.79, B:H.79, B:H.79, B:H.79

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

SO4.2: 10 residues within 4Å: Chain A: Y.40 Chain B: I.110, P.111, G.112, S.113, G.114, K.115, T.116, E.133, R.175 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.112, B:G.112, B:S.113, B:G.114, B:K.115, B:T.116, B:E.133 Water bridges: B:S.117 Salt bridges: B:K.115, B:R.175 SO4.3: 4 residues within 4Å: Chain B: N.76, S.184, G.269, S.270 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.76, B:S.184, B:S.270, B:S.270

1 x FLC: CITRATE ANION(Non-covalent)

FLC.4: 7 residues within 4Å: Chain B: A.137, R.138, P.139, Q.140, N.194, D.197, Q.201 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.137, B:Q.140, B:Q.140, B:Q.201 Salt bridges: B:R.138, B:R.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rocker, A. et al., The ng_ zeta 1 toxin of the gonococcal epsilon/zeta toxin/antitoxin system drains precursors for cell wall synthesis. Nat Commun (2018)

Release Date

2018-05-02

Peptides

Epsilon_1 antitoxin: A
Zeta_1 toxin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Epsilon_1 antitoxin

Zeta_1 toxin

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