SMTL ID : 4i52.2 (2 other biounits)

scMenB im complex with 1-hydroxy-2-naphthoyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-trimer

Ligands

3 x 1HA: 1-hydroxy-2-naphthoyl-CoA(Non-covalent)

1HA.1: 24 residues within 4Å: Chain A: H.29, K.30, R.31, A.33, F.34, S.75, G.76, G.77, D.78, Q.79, Y.87, L.96, V.98, L.99, Y.119, I.121, G.122, G.123, T.145, V.149, S.151, F.152, D.153 Ligands: CL.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.34, A:Y.87, A:L.96, A:V.98, A:L.99, A:Y.119, A:I.121, A:I.121, A:D.153 Hydrogen bonds: A:S.75, A:S.75, A:G.77, A:G.77, A:Q.79, A:Y.119, A:G.123, A:T.145, A:S.151 Salt bridges: A:R.31, A:R.31 1HA.3: 23 residues within 4Å: Chain B: H.29, K.30, R.31, A.33, F.34, S.75, G.76, G.77, D.78, Q.79, Y.87, L.96, V.98, L.99, Y.119, I.121, G.123, T.145, V.149, S.151, F.152, Q.179 Ligands: CL.4 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:F.34, B:Y.87, B:L.96, B:V.98, B:L.99, B:Y.119, B:I.121, B:I.121, B:I.121 Hydrogen bonds: B:S.75, B:S.75, B:G.77, B:G.77, B:D.78, B:Q.79, B:Y.119, B:G.123, B:T.145, B:S.151, B:F.152 Salt bridges: B:R.31, B:R.31 1HA.5: 25 residues within 4Å: Chain C: H.29, K.30, R.31, A.33, F.34, S.75, G.76, G.77, D.78, Q.79, Y.87, L.96, V.98, L.99, Y.119, I.121, G.122, G.123, T.145, V.149, S.151, F.152, D.153, Q.179 Ligands: CL.6 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:F.34, C:Y.87, C:L.96, C:V.98, C:L.99, C:Y.119, C:I.121, C:D.153 Hydrogen bonds: C:S.75, C:S.75, C:G.77, C:G.77, C:Q.79, C:Q.79, C:Y.119, C:Y.119, C:G.123, C:T.145, C:S.151, C:F.152 Water bridges: C:H.29, C:K.30, C:K.30, C:R.31, C:R.31 Salt bridges: C:R.31, C:R.31

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: G.122, Q.144, T.145, G.146, W.174 Ligands: 1HA.1 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain B: G.122, Q.144, T.145, G.146, W.174 Ligands: 1HA.3 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain C: G.122, Q.144, T.145, G.146, W.174 Ligands: 1HA.5 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Y. et al., Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme a synthase from the crotonase fold superfamily. Plos One (2013)

Release Date

2013-05-08

Peptides

Naphthoate synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
F

Naphthoate synthase

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