SMTL ID : 1u8v.1

Crystal Structure of 4-Hydroxybutyryl-CoA Dehydratase from Clostridium aminobutyricum: Radical catalysis involving a [4Fe-4S] cluster and flavin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

SF4.1: 9 residues within 4Å: Chain A: C.99, F.100, Q.101, C.103, H.292, S.295, Y.296, C.299, E.455 6 PLIP interactions: 6 interactions with chain A, Salt bridges: A:E.455 pi-Cation interactions: A:F.100 Metal complexes: A:C.99, A:C.103, A:H.292, A:C.299 SF4.3: 9 residues within 4Å: Chain B: C.99, F.100, Q.101, C.103, H.292, S.295, Y.296, C.299, E.455 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Water interactions Salt bridges: B:E.455 pi-Cation interactions: B:F.100 Metal complexes: B:C.99, B:C.103, B:H.292, B:C.299, H2O.42 SF4.5: 10 residues within 4Å: Chain C: C.99, F.100, Q.101, C.103, V.104, H.292, S.295, Y.296, C.299, E.455 6 PLIP interactions: 6 interactions with chain C, Salt bridges: C:E.455 pi-Cation interactions: C:F.100 Metal complexes: C:C.99, C:C.103, C:H.292, C:C.299 SF4.7: 10 residues within 4Å: Chain D: C.99, F.100, Q.101, C.103, V.104, H.292, S.295, Y.296, C.299, E.455 6 PLIP interactions: 6 interactions with chain D, Salt bridges: D:E.455 pi-Cation interactions: D:F.100 Metal complexes: D:C.99, D:C.103, D:H.292, D:C.299

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 23 residues within 4Å: Chain A: M.149, T.150, K.153, R.156, H.188, Q.189, T.190, E.257, V.450, E.455, H.458, A.460, G.461, S.462, Q.464 Chain B: A.320, A.323, H.325, D.386, I.387, G.389, G.390, V.393 36 PLIP interactions: 30 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.450, A:E.455, A:E.455, B:V.393 Hydrogen bonds: A:M.149, A:T.150, A:T.150, A:T.150, A:R.156, A:Q.189, A:Q.189, A:T.190, A:T.190, A:A.460, A:G.461, A:S.462, B:D.386, B:G.390 Water bridges: A:T.150, A:K.153, A:K.153, A:K.153, A:R.156, A:R.156, A:R.156, A:H.188, A:S.462, A:Q.464, B:N.318, B:D.386, B:L.391 Salt bridges: A:K.153, A:K.153, A:R.156, A:R.156, A:H.188 FAD.4: 22 residues within 4Å: Chain A: A.320, A.323, H.325, D.386, I.387, G.389, G.390, V.393 Chain B: M.149, T.150, K.153, R.156, H.188, Q.189, T.190, E.257, V.450, E.455, H.458, A.460, G.461, S.462 38 PLIP interactions: 31 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:H.188, B:E.257, B:V.450, B:E.455, B:E.455, A:V.393 Hydrogen bonds: B:M.149, B:T.150, B:T.150, B:T.150, B:R.156, B:Q.189, B:Q.189, B:T.190, B:A.460, B:G.461, B:S.462, A:D.386, A:G.390 Water bridges: B:T.150, B:P.152, B:K.153, B:K.153, B:K.153, B:R.156, B:R.156, B:R.156, B:T.190, B:S.462, A:N.318, A:H.325, A:D.386, A:L.391 Salt bridges: B:K.153, B:K.153, B:R.156, B:R.156, B:H.188 FAD.6: 23 residues within 4Å: Chain C: M.149, T.150, K.153, R.156, H.188, Q.189, T.190, E.257, V.450, E.455, H.458, A.460, G.461, S.462, Q.464 Chain D: A.320, A.323, H.325, D.386, I.387, G.389, G.390, V.393 39 PLIP interactions: 32 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:H.188, C:V.450, C:E.455, C:E.455, D:V.393 Hydrogen bonds: C:M.149, C:T.150, C:T.150, C:T.150, C:R.156, C:Q.189, C:Q.189, C:T.190, C:A.460, C:G.461, C:S.462, D:D.386, D:G.390 Water bridges: C:T.150, C:K.153, C:K.153, C:K.153, C:R.156, C:R.156, C:R.156, C:H.188, C:T.190, C:S.462, C:Q.464, C:A.465, D:N.318, D:N.318, D:D.386, D:L.391 Salt bridges: C:K.153, C:K.153, C:R.156, C:R.156, C:H.188 FAD.8: 23 residues within 4Å: Chain C: A.320, A.323, H.325, D.386, I.387, G.389, G.390, V.393 Chain D: M.149, T.150, K.153, R.156, H.188, Q.189, T.190, E.257, V.450, E.455, H.458, A.460, G.461, S.462, Q.464 35 PLIP interactions: 30 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:V.450, D:E.455, D:E.455, C:V.393 Hydrogen bonds: D:M.149, D:T.150, D:T.150, D:T.150, D:R.156, D:Q.189, D:T.190, D:T.190, D:H.458, D:A.460, D:G.461, D:S.462, C:D.386, C:G.390 Water bridges: D:G.147, D:P.152, D:K.153, D:R.156, D:R.156, D:R.156, D:E.455, D:S.462, D:S.462, D:Q.464, C:N.318, C:L.391 Salt bridges: D:K.153, D:K.153, D:R.156, D:R.156, D:H.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martins, B.M. et al., Crystal structure of 4-hydroxybutyryl-CoA dehydratase: radical catalysis involving a [4Fe-4S] cluster and flavin. Proc.Natl.Acad.Sci.USA (2004)

Release Date

2004-12-21

Peptides

Gamma-aminobutyrate metabolism dehydratase/isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Gamma-aminobutyrate metabolism dehydratase/isomerase