SMTL ID : 6dlx.1

FtsY-NG domain bound to fragment 3.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

4 x GXY: 4-bromo-2,5-dimethoxyaniline(Non-covalent)

GXY.1: 7 residues within 4Å: Chain A: D.165, A.167, S.168, K.205, R.208, V.209, K.212 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.209 Hydrogen bonds: A:K.212 GXY.2: 9 residues within 4Å: Chain A: T.113, T.114, G.117, K.118, Q.145, L.146, W.149, R.152, I.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.118, A:Q.145 pi-Stacking: A:W.149 GXY.12: 7 residues within 4Å: Chain B: D.165, A.167, S.168, F.171, K.205, V.209, K.212 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.209 Hydrogen bonds: B:K.205, B:K.212 GXY.13: 10 residues within 4Å: Chain B: T.113, T.114, I.116, G.117, K.118, L.132, Q.145, L.146, W.149, R.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.117, B:W.149

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

NH4.3: 4 residues within 4Å: Chain A: R.25, G.26, E.71 Chain B: G.127 Ligand excluded by PLIP NH4.4: 1 residues within 4Å: Chain A: Q.125 Ligand excluded by PLIP NH4.5: 5 residues within 4Å: Chain A: G.1, F.2, A.3, R.4, R.7 Ligand excluded by PLIP NH4.6: 3 residues within 4Å: Chain A: Q.160, S.168, D.172 Ligand excluded by PLIP NH4.7: 10 residues within 4Å: Chain A: M.104, V.105, G.106, K.112, T.189, A.190, G.191, L.199, L.203, F.240 Ligand excluded by PLIP NH4.8: 7 residues within 4Å: Chain A: A.134, G.135, D.136, A.142, V.143, L.146, D.188 Ligand excluded by PLIP NH4.9: 5 residues within 4Å: Chain A: F.138, G.163, A.164, D.165, S.166 Ligand excluded by PLIP NH4.10: 6 residues within 4Å: Chain A: M.104, V.105, K.112, M.222, L.223, T.224 Ligand excluded by PLIP NH4.14: 8 residues within 4Å: Chain B: A.98, P.99, V.101, I.174, K.178, D.214, A.217, H.219 Ligand excluded by PLIP NH4.15: 9 residues within 4Å: Chain B: A.134, D.136, T.137, V.143, A.159, Q.160, H.161, A.164, V.169 Ligand excluded by PLIP NH4.16: 4 residues within 4Å: Chain B: I.29, A.62, S.63, Q.66 Ligand excluded by PLIP NH4.17: 3 residues within 4Å: Chain B: V.157, I.158, A.159 Ligand excluded by PLIP NH4.18: 5 residues within 4Å: Chain B: G.150, N.154, I.155, P.156, R.180 Ligand excluded by PLIP NH4.19: 7 residues within 4Å: Chain B: N.108, G.109, V.110, G.111, K.112, T.113, T.114 Ligand excluded by PLIP NH4.20: 3 residues within 4Å: Chain B: Q.175, K.178, A.179 Ligand excluded by PLIP NH4.21: 9 residues within 4Å: Chain B: G.106, V.107, V.110, L.223, T.224, I.225, Q.236, F.240 Ligands: NH4.22 Ligand excluded by PLIP NH4.22: 8 residues within 4Å: Chain B: V.107, V.110, I.225, D.226, T.229, A.233, Q.236 Ligands: NH4.21 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 5 residues within 4Å: Chain A: I.21, Y.74, A.300 Chain B: Q.125, E.284 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.300 Water bridges: A:E.71, B:Q.125, B:Q.125, B:Q.125

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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