SMTL ID : 4ehu.1

Activator of the 2-Hydroxyisocaproyl-CoA Dehydratase from Clostridium difficile with bound ADPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: C.125, A.126, A.127, C.164, T.165, V.166 Chain B: K.124, C.125, A.126, A.127, C.164, T.165, V.166 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, Metal complexes: A:C.125, A:C.164, B:C.125, B:C.164

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 25 residues within 4Å: Chain A: G.9, S.10, T.11, A.12, K.14, Y.65, E.79, G.101, G.102, Q.103, D.104, G.130, R.131, L.133, D.134, V.144, S.145, G.214, G.215, V.216, R.218, N.219, Q.241 Ligands: MG.3, NA.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.10, A:S.10, A:T.11, A:T.11, A:A.12, A:K.14, A:G.102, A:Q.103, A:D.104, A:D.104, A:D.134, A:G.215, A:R.218, A:Q.241 Water bridges: A:E.79, A:G.101, A:Q.103, A:K.106, A:R.218, A:R.218, A:R.218, A:R.218 Salt bridges: A:K.14 ANP.8: 24 residues within 4Å: Chain B: G.9, S.10, T.11, A.12, K.14, Y.65, E.79, G.101, G.102, Q.103, D.104, G.130, R.131, L.133, D.134, V.144, S.145, G.214, G.215, V.216, R.218, N.219, Q.241 Ligands: MG.9 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:G.9, B:G.9, B:S.10, B:S.10, B:S.10, B:T.11, B:A.12, B:K.14, B:G.102, B:Q.103, B:Q.103, B:D.104, B:D.134, B:G.215, B:R.218, B:Q.241 Water bridges: B:E.79, B:G.101, B:K.106, B:K.106, B:R.218, B:R.218, B:N.219, B:Q.241 Salt bridges: B:K.14

2 x MG: MAGNESIUM ION(Non-functional Binders)

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

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

ACT.4: 4 residues within 4Å: Chain A: I.139, I.140, E.141, L.176 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.176 Water bridges: A:L.176 ACT.7: 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 Hydrophobic interactions: A:A.187 Water bridges: A:H.190 Salt bridges: A:R.224 ACT.10: 4 residues within 4Å: Chain B: R.131, D.134, V.135, K.138 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.138 Water bridges: B:R.131, B:R.131 Salt bridges: B:R.131

3 x NA: SODIUM ION(Non-functional Binders)

NA.5: 5 residues within 4Å: Chain A: T.11, A.12, S.31, Q.241 Ligands: ANP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.31, A:Q.241 Water bridges: A:S.31 NA.6: 5 residues within 4Å: Chain A: R.218, I.239, P.240, Q.241, L.242 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.241 Water bridges: A:R.218, A:D.238, A:Q.241 NA.11: 5 residues within 4Å: Chain B: R.218, I.239, P.240, Q.241, L.242 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.239, B:Q.241 Water bridges: B:R.218

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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