SMTL ID : 4eht.1

Activator of the 2-Hydroxyisocaproyl-CoA dehydratase from Clostridium difficile with bound ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain A: C.125, A.126, A.127, C.164, T.165, V.166 Chain B: C.125, A.126, A.127, C.164, T.165, V.166 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, Metal complexes: B:C.125, B:C.164, A:C.125, A:C.164

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 19 residues within 4Å: Chain A: G.9, S.10, T.11, A.12, K.14, G.101, G.102, G.130, D.134, V.144, S.145, G.214, G.215, V.216, R.218, N.219, Q.241 Ligands: MG.3, CL.7 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.10, A:T.11, A:A.12, A:G.102, A:D.134, A:G.215, A:R.218, A:Q.241 Water bridges: A:S.10, A:S.10, A:K.14, A:K.14, A:G.102, A:D.134, A:S.145, A:G.214, A:R.218, A:R.218, A:R.218, A:R.218, A:R.218 Salt bridges: A:K.14, A:K.14 ADP.8: 21 residues within 4Å: Chain B: G.9, S.10, T.11, A.12, K.14, G.101, G.102, Q.103, G.130, L.133, D.134, V.144, S.145, G.214, G.215, V.216, R.218, N.219, Q.241 Ligands: MG.9, NH4.11 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.9, B:S.10, B:T.11, B:A.12, B:G.102, B:D.134, B:G.215, B:R.218, B:Q.241 Water bridges: B:S.10, B:T.11, B:K.14, B:K.14, B:K.14, B:K.14, B:G.102, B:Q.103, B:Q.103, B:S.145, B:S.145, B:N.219 Salt bridges: B:K.14, B:K.14

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.14, E.79, H.83 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain B: K.14, E.79, H.83 Ligands: ADP.8 No protein-ligand interaction detected (PLIP)

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

ACT.4: 8 residues within 4Å: Chain A: S.151, M.152, S.154, A.187, H.190, G.221, R.224, R.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.151 Water bridges: A:H.190 Salt bridges: A:R.224 ACT.5: 7 residues within 4Å: Chain A: S.81, A.84, L.110, G.114, R.115, L.116, Y.251 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.84 Hydrogen bonds: A:L.116 Water bridges: A:S.81 Salt bridges: A:R.115 ACT.10: 7 residues within 4Å: Chain B: T.29, R.218, D.238, I.239, P.240, Q.241, L.242 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.241 Hydrogen bonds: B:Q.241, B:L.242 Water bridges: B:D.238 Salt bridges: B:R.218

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

CL.6: 5 residues within 4Å: Chain A: R.218, I.239, P.240, Q.241, L.242 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: T.11, A.12, S.31, Q.241 Ligands: ADP.2 Ligand excluded by PLIP

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.11: 6 residues within 4Å: Chain B: T.11, A.12, T.29, S.31, Q.241 Ligands: ADP.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.31, B:Q.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knauer, S.H. et al., On the ATP-Dependent Activation of the Radical Enzyme (R)-2-Hydroxyisocaproyl-CoA Dehydratase. Biochemistry (2012)

Release Date

2012-08-08

Peptides

Activator of 2-hydroxyisocaproyl-CoA dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Activator of 2-hydroxyisocaproyl-CoA dehydratase

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