SMTL ID : 4ac9.3 (3 other biounits)

CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS IN COMPLEX WITH GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.03 Å

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 14 residues within 4Å: Chain A: H.27, I.28, D.29, H.30, G.31, K.32, T.33, T.34, K.134, D.136, S.169, A.170, K.171 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:D.29, A:H.30, A:G.31, A:K.32, A:T.33, A:T.34, A:T.34, A:K.134, A:K.134, A:A.170, A:K.171 Water bridges: A:K.32, A:K.32, A:T.33, A:T.33, A:T.33 Salt bridges: A:K.32, A:D.136 pi-Cation interactions: A:K.50, A:K.50

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.33 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.33, H2O.1, H2O.2, H2O.3, H2O.4

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

SO4.3: 7 residues within 4Å: Chain A: D.122, H.123, K.298, I.299, S.300, D.301 Ligands: SO4.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.122, A:D.301, A:D.301 Salt bridges: A:H.123, A:K.298 SO4.4: 4 residues within 4Å: Chain A: H.158, K.161, D.301 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.158, A:K.161 SO4.5: 4 residues within 4Å: Chain A: K.432, L.478, R.479, R.480 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.480, A:R.480 Salt bridges: A:K.432, A:R.479 SO4.6: 4 residues within 4Å: Chain A: H.27, K.111, T.112, Q.113 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.112, A:T.112, A:Q.113 Salt bridges: A:H.27, A:K.111 SO4.13: 1 residues within 4Å: Chain A: N.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.306

6 x DXC: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID(Non-covalent)

DXC.7: 11 residues within 4Å: Chain A: I.61, D.62, I.63, G.64, F.65, S.66, V.216, S.245, Q.247, G.263, M.264 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.61, A:I.63, A:I.63, A:F.65, A:F.65, A:V.216, A:V.216 Hydrogen bonds: A:I.63, A:G.64, A:F.65, A:S.66, A:S.245, A:S.245, A:Q.247 DXC.8: 4 residues within 4Å: Chain A: R.12, P.13, H.14, M.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.15 Hydrogen bonds: A:M.15 DXC.9: 8 residues within 4Å: Chain A: P.110, T.112, G.115, R.145, I.153, K.304, T.380, L.382 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.112, A:I.153, A:L.382 Salt bridges: A:R.145 DXC.10: 9 residues within 4Å: Chain A: S.135, D.136, A.138, G.139, T.140, S.169, T.172, F.174 Ligands: DXC.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.136, A:F.174, A:F.174, A:F.174, A:F.174 DXC.11: 6 residues within 4Å: Chain A: T.140, I.143, K.144, E.147, F.174 Ligands: DXC.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.143 DXC.12: 6 residues within 4Å: Chain A: D.301, F.303, K.304, E.345, I.347, S.348 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.347 Hydrogen bonds: A:K.304, A:E.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leibundgut, M. et al., Selenocysteine tRNA-Specific Elongation Factor Selb is a Structural Chimaera of Elongation and Initiation Factors. Embo J. (2005)

Release Date

2012-08-22

Peptides

MJ0495-LIKE PROTEIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

MJ0495-LIKE PROTEIN

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