SMTL ID : 2j7p.1 (1 other biounit)

GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: R.128, E.179, R.181 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.128, A:R.181 EDO.2: 2 residues within 4Å: Chain A: Q.137 Chain B: E.263 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.137 EDO.10: 6 residues within 4Å: Chain B: L.236, V.259, P.270, F.271, D.272, F.276 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.272, B:D.272 EDO.11: 8 residues within 4Å: Chain A: L.106, L.192, Q.193, V.229 Chain B: V.210, G.238, T.239, A.240 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.239, B:A.240, A:Q.193

8 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 2 residues within 4Å: Chain A: K.123, R.181 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: R.286, L.287 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: S.164, P.165 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: R.191 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: G.18 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain B: S.26, A.27, R.250 Ligand excluded by PLIP IOD.13: 4 residues within 4Å: Chain B: W.3, G.4, L.43, K.44 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain B: K.44, E.45, K.48 Ligand excluded by PLIP

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

GNP.8: 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.90, G.91, R.121, L.175 Ligands: MG.9, GNP.15 24 PLIP interactions: 20 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.108, A:G.110, A:K.111, A:K.111, A:T.112, A:T.112, A:T.113, A:T.113, A:K.117, A:D.135, A:R.138, A:R.138, A:Q.144, A:G.190, A:K.246, A:S.273, B:N.90 Water bridges: A:T.112, A:R.138, A:E.274, B:N.90, B:G.173, B:G.173 Salt bridges: A:D.248 GNP.15: 23 residues within 4Å: Chain A: Q.107, R.138 Chain B: N.90, G.91, V.92, G.93, K.94, T.95, T.96, K.100, D.118, R.121, Q.127, G.173, T.234, K.235, D.237, G.260, V.261, G.262, E.263 Ligands: GNP.8, MG.16 28 PLIP interactions: 23 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.91, B:V.92, B:G.93, B:K.94, B:K.94, B:T.95, B:T.96, B:T.96, B:K.100, B:R.121, B:R.121, B:Q.127, B:Q.127, B:G.173, B:K.235, B:G.262 Water bridges: B:T.95, B:T.95, B:T.96, B:R.121, B:R.121, A:R.138, A:R.138, A:G.190, A:G.190 Salt bridges: B:D.237, B:E.263, A:R.138

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain A: T.112 Ligands: GNP.8 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.112, H2O.3, H2O.4, H2O.4 MG.16: 3 residues within 4Å: Chain B: T.95, R.121 Ligands: GNP.15 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.95, H2O.8, H2O.8, H2O.9

1 x K: POTASSIUM ION(Non-covalent)

K.17: 3 residues within 4Å: Chain B: L.236, G.238, A.240 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:G.238, B:A.240, H2O.7, H2O.10, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gawronski-Salerno, J. et al., Structure of the Gmppnp-Stabilized Ng Domain Complex of the Srp Gtpases Ffh and Ftsy. J.Struct.Biol. (2007)

Release Date

2006-12-11

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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