SMTL ID : 1okk.1

HOMO-HETERODIMERIC COMPLEX OF THE SRP GTPASES

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.1: 25 residues within 4Å: Chain A: L.106, Q.107, G.108, S.109, G.110, K.111, T.112, T.113, K.117, D.135, R.138, Q.144, G.190, K.246, D.248, G.271, V.272, S.273, E.274 Chain B: N.110, G.111, R.141, L.195 Ligands: MG.2, GCP.15 27 PLIP interactions: 25 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.108, A:G.110, A:K.111, A:K.111, A:T.112, A:T.113, A:T.113, A:K.117, A:R.138, A:Q.144, A:Q.144, A:G.190, A:K.246, A:S.273, A:E.274, B:N.110 Water bridges: A:T.112, A:T.112, A:T.112, A:T.113, A:E.274, A:E.274, A:E.274, A:E.274, B:N.110 Salt bridges: A:D.248 pi-Cation interactions: A:K.246 GCP.15: 23 residues within 4Å: Chain A: Q.107, R.138 Chain B: V.109, 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.255, D.257, G.280, V.281, G.282, E.283 Ligands: GCP.1, MG.16 25 PLIP interactions: 23 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.111, B:G.113, B:K.114, B:K.114, B:T.115, B:T.116, B:T.116, B:K.120, B:D.138, B:R.141, B:Q.147, B:Q.147, B:G.193, B:K.255, B:G.282 Water bridges: B:T.115, B:T.115, B:T.115, B:T.115, B:T.116, B:R.141, A:R.138 Salt bridges: B:D.257, B:E.283, A:R.138

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.112 Ligands: GCP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.112, H2O.8, H2O.8, H2O.10 MG.16: 3 residues within 4Å: Chain B: T.115, R.141 Ligands: GCP.15 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.115, H2O.17, H2O.19, H2O.22

2 x BZP: N1-CARBOXYPIPERAZINE(Non-covalent)

BZP.3: 10 residues within 4Å: Chain A: L.247, A.270, V.272, E.280, P.281, F.282, Y.283, R.286, R.290 Ligands: SO4.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.280, A:Y.283, A:Y.283, A:R.290 Water bridges: A:R.286 BZP.4: 3 residues within 4Å: Chain A: K.96, D.97, R.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.97, A:R.98

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

SO4.5: 2 residues within 4Å: Chain A: G.20, R.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.21 Water bridges: A:R.21, A:R.21 Salt bridges: A:R.21 SO4.6: 3 residues within 4Å: Chain A: R.32, R.35, R.49 8 PLIP interactions: 8 interactions with chain A Water bridges: A:K.28, A:K.28, A:R.32, A:R.32, A:R.49 Salt bridges: A:R.32, A:R.35, A:R.49 SO4.7: 5 residues within 4Å: Chain A: P.139, A.140, A.141, R.142, E.143 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.140, A:A.141, A:R.142, A:E.143 Water bridges: A:E.143 Salt bridges: A:R.142 SO4.8: 3 residues within 4Å: Chain A: R.286, R.290 Ligands: BZP.3 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.286, A:R.290 SO4.9: 4 residues within 4Å: Chain A: S.67, L.68, T.69, V.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.68, A:T.69 Water bridges: A:T.69 SO4.10: 4 residues within 4Å: Chain A: S.164, E.166, S.167, R.170 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.164, A:S.164 Water bridges: A:S.164, A:S.164 Salt bridges: A:R.170 SO4.11: 2 residues within 4Å: Chain A: R.128, R.181 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.128, A:R.181 SO4.12: 3 residues within 4Å: Chain A: E.166, R.169, R.170 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.169, A:R.169 Salt bridges: A:R.169, A:R.170 SO4.13: 1 residues within 4Å: Chain A: R.231 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.231 Salt bridges: A:R.231 SO4.14: 3 residues within 4Å: Chain A: R.142, M.160, D.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.161, A:D.161 Salt bridges: A:R.142 SO4.17: 3 residues within 4Å: Chain B: R.123, R.154, P.285 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.154 Salt bridges: B:R.123, B:R.154

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

EDO.18: 8 residues within 4Å: Chain A: L.106, L.192, Q.193, V.229 Chain B: V.230, G.258, T.259, A.260 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.259, B:T.259, B:A.260, A:Q.193 EDO.19: 2 residues within 4Å: Chain B: K.214 Ligands: EDO.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.214 EDO.20: 3 residues within 4Å: Chain B: Y.173, K.214 Ligands: EDO.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.214 Water bridges: B:A.170 EDO.21: 4 residues within 4Å: Chain A: P.139 Chain B: E.150, W.151, R.154 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.154 Water bridges: B:E.150, B:E.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Focia, P.J. et al., Heterodimeric Gtpase Core of the Srp Targeting Complex. Science (2004)

Release Date

2004-01-19

Peptides

SIGNAL RECOGNITION PARTICLE PROTEIN: A
CELL DIVISION PROTEIN FTSY: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

SIGNAL RECOGNITION PARTICLE PROTEIN

CELL DIVISION PROTEIN FTSY

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