SMTL ID : 5l3s.3 (3 other biounits)

Structure of the GTPase heterodimer of crenarchaeal SRP54 and FtsY

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 26 residues within 4Å: Chain A: V.110, Q.111, G.112, S.113, G.114, K.115, T.116, T.117, K.121, D.139, R.142, Q.148, G.194, T.251, K.252, D.254, G.277, T.278, G.279, E.280 Chain B: N.110, G.111, R.141, M.195 Ligands: MG.2, GNP.7 30 PLIP interactions: 24 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.112, A:G.114, A:K.115, A:K.115, A:T.116, A:T.117, A:T.117, A:T.117, A:K.121, A:D.139, A:R.142, A:Q.148, A:G.194, A:K.252, A:G.279, A:E.280, B:N.110, B:N.110, B:N.110 Water bridges: A:T.116, A:T.116, A:T.116, A:R.142, B:G.193, B:G.193, B:M.195 Salt bridges: A:R.142, A:D.254, A:E.280 pi-Cation interactions: A:K.252 GNP.7: 25 residues within 4Å: Chain A: Q.111, G.112, R.142, H.196, E.201 Chain B: N.110, G.111, V.112, G.113, K.114, T.115, T.116, K.120, D.138, R.141, Q.147, G.193, K.249, D.251, G.274, V.275, G.276, Q.277 Ligands: GNP.1, MG.8 25 PLIP interactions: 19 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:G.111, B:G.113, B:K.114, B:K.114, B:T.115, B:T.115, B:T.116, B:T.116, B:T.116, B:K.120, B:R.141, B:Q.147, B:G.193, B:K.249, B:K.249, B:G.276, B:Q.277, A:H.196 Water bridges: B:R.141, A:R.142, A:R.142, A:R.142 Salt bridges: B:D.251, A:R.142, A:E.201

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.116 Ligands: GNP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.116, H2O.1, H2O.2, H2O.2 MG.8: 3 residues within 4Å: Chain B: T.115, R.141 Ligands: GNP.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.115, H2O.7, H2O.7, H2O.7

1 x G: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

G.3: 12 residues within 4Å: Chain A: V.140, Y.141, R.142, P.143, A.144, A.145, Y.146, D.147, P.164, Q.167 Chain B: Y.150, K.154 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.141, A:A.144, A:A.145, A:Y.146, A:D.147, A:Q.167, B:Y.150 Water bridges: A:D.147, B:K.154, B:K.154

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: M.253, I.276, F.288, N.289, R.292, F.293, R.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.289, A:N.289, A:R.296 Water bridges: A:E.286 GOL.5: 7 residues within 4Å: Chain A: L.152, Q.155, E.280, K.281, I.282 Chain B: F.140, A.142 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.155, A:I.282, B:F.140 Water bridges: B:A.142, B:A.142 GOL.9: 4 residues within 4Å: Chain B: Y.150, Q.277, N.278, Y.279 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.279 Water bridges: B:D.280

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

SO4.6: 4 residues within 4Å: Chain A: Y.198, G.199, R.238 Chain B: D.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.199 Water bridges: A:R.238 Salt bridges: A:R.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wild, K. et al., Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex. J.Mol.Biol. (2016)

Release Date

2016-06-08

Peptides

Signal recognition particle 54 kDa protein: A
Signal recognition particle receptor FtsY: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Signal recognition particle 54 kDa protein

Signal recognition particle receptor FtsY

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