SMTL ID : 3bbd.1

M. jannaschii Nep1 complexed with S-adenosyl-homocysteine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 17 residues within 4Å: Chain A: M.141, T.142, K.143, I.161, G.162, F.164, P.165, G.167, I.183, S.184, I.185, Y.186, K.188, G.189, L.190, A.192, V.195 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.162, A:G.167, A:G.167, A:I.185, A:Y.186, A:Y.186, A:L.190 Water bridges: A:T.142 Salt bridges: A:K.143 SAH.6: 17 residues within 4Å: Chain B: M.141, T.142, K.143, I.161, G.162, F.164, P.165, G.167, I.183, S.184, I.185, Y.186, K.188, G.189, L.190, A.192, V.195 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.162, B:G.167, B:I.185, B:Y.186, B:Y.186, B:L.190 Water bridges: B:T.142 Salt bridges: B:K.143

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: D.128, E.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.132 Water bridges: A:D.128, A:D.128 GOL.3: 6 residues within 4Å: Chain A: T.2, N.4, N.77, I.133, N.134, D.157 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.2, A:N.4, A:N.77, A:N.134 Water bridges: A:N.134 GOL.4: 7 residues within 4Å: Chain A: Y.79, V.87, E.122, K.124, L.129, E.132, I.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.79, A:E.132, A:E.132 Water bridges: A:E.132 GOL.5: 6 residues within 4Å: Chain A: N.71, H.72, K.74, P.92, E.93 Chain B: K.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.71, A:P.92 GOL.7: 5 residues within 4Å: Chain B: Y.79, K.89, E.122, E.132, I.133 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.79, B:K.89, B:E.122, B:E.132 GOL.8: 7 residues within 4Å: Chain A: Y.201, S.202, F.205 Chain B: P.150, I.198, Y.201, S.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.198 GOL.9: 5 residues within 4Å: Chain B: T.2, N.4, I.133, N.134, D.157 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.4, B:I.133 Water bridges: B:N.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taylor, A.B. et al., The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site. Nucleic Acids Res. (2008)

Release Date

2008-02-05

Peptides

Ribosome biogenesis protein NEP1-like: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosome biogenesis protein NEP1-like

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