SMTL ID : 1ob5.1

T. aquaticus elongation factor EF-Tu complexed with the antibiotic enacyloxin IIa, a GTP analog, and Phe-tRNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-trimer

Ligands

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

GNP.1: 21 residues within 4Å: Chain A: V.20, D.21, G.23, K.24, T.25, T.26, Y.47, G.60, I.61, T.62, P.83, G.84, H.85, N.136, K.137, D.139, M.140, S.174, A.175, L.176 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:D.21, A:G.23, A:K.24, A:K.24, A:T.25, A:T.25, A:T.26, A:T.26, A:Y.47, A:T.62, A:T.62, A:T.62, A:T.62, A:G.84, A:H.85, A:N.136, A:K.137, A:S.174, A:A.175, A:L.176 Salt bridges: A:D.139 GNP.4: 21 residues within 4Å: Chain C: V.20, D.21, G.23, K.24, T.25, T.26, Y.47, G.60, I.61, T.62, P.83, G.84, H.85, N.136, K.137, D.139, M.140, S.174, A.175, L.176 Ligands: MG.5 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:D.21, C:G.23, C:K.24, C:K.24, C:T.25, C:T.25, C:T.26, C:T.26, C:Y.47, C:T.62, C:T.62, C:T.62, C:T.62, C:G.84, C:H.85, C:N.136, C:K.137, C:S.174, C:A.175, C:L.176 Salt bridges: C:D.139 GNP.7: 21 residues within 4Å: Chain E: V.20, D.21, G.23, K.24, T.25, T.26, Y.47, G.60, I.61, T.62, P.83, G.84, H.85, N.136, K.137, D.139, M.140, S.174, A.175, L.176 Ligands: MG.8 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:D.21, E:G.23, E:K.24, E:K.24, E:T.25, E:T.25, E:T.26, E:T.26, E:Y.47, E:T.62, E:T.62, E:T.62, E:T.62, E:G.84, E:H.85, E:N.136, E:K.137, E:S.174, E:A.175, E:L.176 Salt bridges: E:D.139

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.24, T.25, T.62, D.81, C.82 Ligands: GNP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.25, A:T.62, A:C.82 MG.5: 6 residues within 4Å: Chain C: K.24, T.25, T.62, D.81, C.82 Ligands: GNP.4 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.25, C:T.62, C:C.82 MG.8: 6 residues within 4Å: Chain E: K.24, T.25, T.62, D.81, C.82 Ligands: GNP.7 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.25, E:T.62, E:C.82

3 x ENX: ENACYLOXIN IIA(Non-covalent)

ENX.3: 20 residues within 4Å: Chain A: R.117, L.121, R.124, Q.125, V.126, G.127, Q.160, Y.161, E.162, L.323, K.325, E.326, E.327, G.328, Y.343, R.345, R.385, F.386, A.387, A.397 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.161, A:Y.161, A:L.323, A:Y.343, A:A.387, A:A.397 Hydrogen bonds: A:Q.125, A:G.127, A:Y.161, A:E.326 Salt bridges: A:R.117, A:K.325 ENX.6: 20 residues within 4Å: Chain C: R.117, L.121, R.124, Q.125, V.126, G.127, Q.160, Y.161, E.162, L.323, K.325, E.326, E.327, G.328, Y.343, R.345, R.385, F.386, A.387, A.397 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.121, C:Y.161, C:Y.161, C:L.323, C:Y.343, C:A.387, C:A.397 Hydrogen bonds: C:Q.125, C:G.127, C:Y.161, C:E.326 Salt bridges: C:R.117, C:K.325 ENX.9: 20 residues within 4Å: Chain E: R.117, L.121, R.124, Q.125, V.126, G.127, Q.160, Y.161, E.162, L.323, K.325, E.326, E.327, G.328, Y.343, R.345, R.385, F.386, A.387, A.397 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:Y.161, E:Y.161, E:L.323, E:Y.343, E:A.387, E:A.397 Hydrogen bonds: E:Q.125, E:G.127, E:Y.161, E:E.326 Salt bridges: E:R.117, E:K.325

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parmeggiani, A. et al., Enacyloxin Iia Pinpoints a Binding Pocket of Elongation Factor TU for Development of Novel Antibiotics. J.Biol.Chem. (2006)

Release Date

2005-10-13

Peptides

ELONGATION FACTOR TU: ACE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

ELONGATION FACTOR TU

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