SMTL ID : 6cvd.1

High resolution crystal structure of FtsY-NG domain of E. coli bound to fragment 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

4 x 4ME: methyl 1H-indole-4-carboxylate(Non-covalent)

4ME.1: 6 residues within 4Å: Chain A: Q.160, S.168, F.171, D.172, V.209, K.212 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.209, A:K.212 Hydrogen bonds: A:K.212 pi-Stacking: A:F.171, A:F.171 4ME.2: 8 residues within 4Å: Chain A: T.113, T.114, G.117, K.118, Q.145, L.146, W.149, I.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.117, A:K.118, A:Q.145 pi-Stacking: A:W.149 4ME.5: 9 residues within 4Å: Chain B: T.113, T.114, I.116, G.117, K.118, Q.145, L.146, W.149, E.281 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.145 Hydrogen bonds: B:W.149 pi-Stacking: B:W.149 4ME.6: 6 residues within 4Å: Chain B: A.167, S.168, F.171, D.172, V.209, K.212 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.209 Hydrogen bonds: B:K.212 Water bridges: B:Q.160 pi-Stacking: B:F.171, B:F.171

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.3: 8 residues within 4Å: Chain A: T.137, V.143, A.159, Q.160, H.161, T.162, G.163, A.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.137 Water bridges: A:Q.160 NH4.4: 7 residues within 4Å: Chain A: A.133, A.134, G.135, D.136, V.143, L.146, D.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.136, A:D.188, A:D.188

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 5 residues within 4Å: Chain B: D.89, E.90, P.91, F.289, K.290 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faoro, C. et al., Discovery of fragments that target key interactions in the signal recognition particle (SRP) as potential leads for a new class of antibiotics. PLoS ONE (2018)

Release Date

2018-08-22

Peptides

Signal recognition particle receptor FtsY: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Signal recognition particle receptor FtsY

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