SMTL ID : 3r9x.1

Crystal structure of Era in complex with MgGDPNP, nucleotides 1506-1542 of 16S ribosomal RNA, and KsgA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.23, I.36, T.44, D.64 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.23, A:T.44, H2O.1, H2O.1

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

GNP.2: 23 residues within 4Å: Chain A: P.18, N.19, V.20, G.21, K.22, S.23, T.24, I.37, S.38, P.39, A.41, G.42, T.43, T.44, G.67, N.129, K.130, D.132, K.133, S.161, A.162, L.163 Ligands: MG.1 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:N.19, A:V.20, A:G.21, A:K.22, A:K.22, A:S.23, A:T.24, A:T.24, A:S.38, A:S.38, A:G.42, A:T.43, A:T.44, A:G.67, A:N.129, A:K.130, A:K.130, A:A.162, A:L.163 Water bridges: A:S.23, A:S.23, A:T.43, A:T.43, A:T.44 Salt bridges: A:D.132

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 6 residues within 4Å: Chain A: P.123, V.124, E.153, T.155, E.156, Y.178 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.123, A:V.124, A:E.156 Hydrogen bonds: A:E.153 MRD.4: 8 residues within 4Å: Chain A: Y.69, E.70, P.71, V.82, E.111, I.112, N.115, F.116 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.70, A:E.70, A:F.116 Hydrogen bonds: A:N.115

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 1 residues within 4Å: Chain B: T.160 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.160 Salt bridges: B:K.130 ACT.6: 4 residues within 4Å: Chain B: K.130, E.134, Q.137, Y.157 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.157 Hydrogen bonds: B:E.134, B:E.134, B:Q.137 Salt bridges: B:K.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tu, C. et al., The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-06-22

Peptides

GTPase Era: A
Ribosomal RNA small subunit methyltransferase A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase Era

Ribosomal RNA small subunit methyltransferase A

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