SMTL ID : 6cy5.1

Crystal structure of Signal recognition particle receptor FtsY from Elizabethkingia anophelis in complex with GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

3 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 17 residues within 4Å: Chain A: V.131, N.132, G.133, V.134, G.135, K.136, T.137, T.138, K.142, T.276, K.277, D.279, G.302, V.303, G.304, E.305 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:V.131, A:G.133, A:V.134, A:G.135, A:K.136, A:T.137, A:T.138, A:T.138, A:K.142, A:K.277, A:G.304 Water bridges: A:N.132, A:K.136, A:T.137, A:T.137, A:T.138, A:T.138, A:K.277 Salt bridges: A:K.136, A:D.279 GDP.3: 8 residues within 4Å: Chain A: D.189, A.191, S.192, F.195, D.196, K.229, V.233, K.236 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.192, A:K.229, A:K.229 Salt bridges: A:D.196, A:K.236, A:K.236 pi-Stacking: A:F.195, A:F.195 GDP.8: 17 residues within 4Å: Chain B: V.131, N.132, G.133, V.134, G.135, K.136, T.137, T.138, K.142, T.276, K.277, D.279, G.302, V.303, G.304, E.305 Ligands: MG.9 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.132, B:G.133, B:V.134, B:G.135, B:K.136, B:T.137, B:T.138, B:T.138, B:K.142, B:K.277, B:G.304 Water bridges: B:N.132, B:T.138, B:T.138, B:K.277, B:D.279, B:D.279, B:E.305 Salt bridges: B:K.136, B:D.279

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.137, D.160 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.137, H2O.3, H2O.3, H2O.4, H2O.10 MG.9: 4 residues within 4Å: Chain B: T.137, D.160, D.212 Ligands: GDP.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.137, H2O.16, H2O.16, H2O.17, H2O.24

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: S.252, K.277, T.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.277, A:K.277 Water bridges: A:S.252 EDO.5: 4 residues within 4Å: Chain A: W.173, R.176, K.306, M.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.176, A:R.176, A:M.307 EDO.6: 4 residues within 4Å: Chain A: K.262, Q.293, F.294, Q.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.295 Water bridges: A:Q.295, A:Q.295 EDO.7: 5 residues within 4Å: Chain A: M.9, V.10, L.107, E.108, P.110 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.10, A:L.107 EDO.10: 4 residues within 4Å: Chain B: W.173, R.176, K.306, M.307 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.176, B:R.176, B:M.307 EDO.11: 5 residues within 4Å: Chain B: G.68, V.69, E.70, Q.255, F.258 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.69, B:Q.255 Water bridges: B:E.70 EDO.12: 3 residues within 4Å: Chain B: V.303, G.304, D.309 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.309 Water bridges: B:E.305 EDO.13: 2 residues within 4Å: Chain B: K.39, A.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.39 Water bridges: B:S.35, B:S.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delker, S.L. et al., Crystal structure of Signal recognition particle receptor FtsY from Elizabethkingia anophelis in complex with GDP. to be published

Release Date

2018-05-02

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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