SMTL ID : 5l3q.1 (1 other biounit)

Structure of the GTPase heterodimer of human SRP54 and SRalpha

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.160, H.284, I.285 Ligands: AMP.5, GOL.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.285 Salt bridges: A:K.160, A:H.284 SO4.6: 2 residues within 4Å: Chain B: R.466, R.470 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.470 SO4.7: 2 residues within 4Å: Chain B: K.496, D.497 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.497 Water bridges: B:D.497 Salt bridges: B:K.496 SO4.8: 2 residues within 4Å: Chain B: T.467, R.470 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.467, B:R.470 Salt bridges: B:R.470 SO4.9: 6 residues within 4Å: Chain B: D.497, A.499, G.500, M.503, K.537, V.541 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.499 Water bridges: B:D.497, B:D.497 Salt bridges: B:K.537

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

GNP.2: 26 residues within 4Å: Chain A: L.115, Q.116, G.117, S.118, G.119, K.120, T.121, T.122, K.126, D.144, R.147, Q.153, G.199, T.254, K.255, D.257, G.280, T.281, G.282, E.283 Chain B: N.427, G.428, R.458, M.525 Ligands: MG.3, GNP.10 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.117, A:G.119, A:K.120, A:K.120, A:K.120, A:T.121, A:T.121, A:T.122, A:T.122, A:T.122, A:K.126, A:R.147, A:Q.153, A:Q.153, A:G.199, A:K.255, A:G.282, B:N.427, B:N.427 Water bridges: A:D.144, A:R.147, A:G.199, A:E.283, B:G.523, B:G.523 Salt bridges: A:D.257, A:E.283 pi-Cation interactions: A:K.255 GNP.10: 26 residues within 4Å: Chain A: Q.116, G.117, R.147, H.201 Chain B: N.427, G.428, V.429, G.430, K.431, S.432, T.433, N.434, K.437, R.458, Q.464, G.523, T.588, K.589, D.591, T.592, G.615, T.616, G.617, Q.618 Ligands: GNP.2, MG.11 30 PLIP interactions: 23 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:G.428, B:V.429, B:G.430, B:K.431, B:K.431, B:K.431, B:S.432, B:T.433, B:T.433, B:N.434, B:K.437, B:R.458, B:Q.464, B:G.523, B:K.589, B:K.589, B:G.617, B:Q.618, A:R.147 Water bridges: B:S.432, B:S.432, B:D.455, B:D.455, A:R.147, A:R.147, A:R.147, A:G.199 Salt bridges: B:D.591, A:R.147 pi-Cation interactions: A:H.201

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: T.121 Ligands: GNP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.121, H2O.1, H2O.1, H2O.1 MG.11: 3 residues within 4Å: Chain B: S.432, D.520 Ligands: GNP.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.432, H2O.2, H2O.2, H2O.2

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: K.292, T.293, Q.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.293, A:T.293, A:Q.294 GOL.12: 6 residues within 4Å: Chain A: K.160 Chain B: F.457, R.458, A.459 Ligands: SO4.1, AMP.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.457, B:A.459, A:K.160

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.5: 7 residues within 4Å: Chain A: E.283, H.284 Chain B: F.457, G.523, L.531 Ligands: SO4.1, GOL.12 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.283, A:E.283 Salt bridges: A:H.284 Water bridges: B:N.427 pi-Stacking: B:F.457, B:F.457

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 subunit alpha: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Signal recognition particle 54 kDa protein

Signal recognition particle receptor subunit alpha

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