SMTL ID : 4izd.1

Crystal structure of DmdD E121A in complex with MMPA-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x 1HE: 3-methylmercaptopropionate-CoA (MMPA-CoA)(Non-covalent)

1HE.1: 13 residues within 4Å: Chain A: D.30, K.31, R.32, A.34, H.66, A.69, L.71, D.72, L.73, V.74, A.114, Y.136, R.144 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.32, A:A.69, A:A.114 Hydrogen bonds: A:L.71, A:L.73 Salt bridges: A:K.31, A:R.32, A:R.32, A:H.66 1HE.2: 25 residues within 4Å: Chain B: D.30, K.31, R.32, A.34, H.66, A.69, G.70, L.71, D.72, L.73, V.74, W.93, A.114, V.116, G.117, G.118, Y.136, P.140, E.141, R.144, I.146, F.147, T.148, G.149 Chain D: F.255 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:A.69, B:L.71, B:A.114, B:V.116, B:E.141 Hydrogen bonds: B:A.69, B:L.71, B:L.71, B:D.72, B:L.73, B:V.74, B:G.118, B:R.144 Salt bridges: B:K.31, B:R.32, B:R.32, B:H.66 pi-Stacking: D:F.255, D:F.255 1HE.3: 13 residues within 4Å: Chain C: D.30, K.31, R.32, A.34, H.66, A.69, L.71, D.72, L.73, V.74, A.114, Y.136, R.144 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:R.32, C:A.69, C:A.114 Hydrogen bonds: C:L.71, C:L.73 Salt bridges: C:K.31, C:R.32, C:R.32, C:H.66 1HE.4: 25 residues within 4Å: Chain D: D.30, K.31, R.32, A.34, H.66, A.69, G.70, L.71, D.72, L.73, V.74, W.93, A.114, V.116, G.117, G.118, Y.136, P.140, E.141, R.144, I.146, F.147, T.148, G.149 Chain F: F.255 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:A.69, D:L.71, D:A.114, D:V.116, D:E.141 Hydrogen bonds: D:A.69, D:L.71, D:L.71, D:L.73, D:V.74, D:G.118, D:E.141, D:R.144 Salt bridges: D:K.31, D:R.32, D:R.32, D:H.66 pi-Stacking: F:F.255, F:F.255 1HE.5: 13 residues within 4Å: Chain E: D.30, K.31, R.32, A.34, H.66, A.69, L.71, D.72, L.73, V.74, A.114, Y.136, R.144 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:R.32, E:A.69, E:A.114 Hydrogen bonds: E:L.71, E:D.72, E:L.73 Salt bridges: E:K.31, E:R.32, E:R.32, E:H.66 1HE.6: 25 residues within 4Å: Chain B: F.255 Chain F: D.30, K.31, R.32, A.34, H.66, A.69, G.70, L.71, D.72, L.73, V.74, W.93, A.114, V.116, G.117, G.118, Y.136, P.140, E.141, R.144, I.146, F.147, T.148, G.149 19 PLIP interactions: 17 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:A.69, F:L.71, F:A.114, F:V.116, F:E.141 Hydrogen bonds: F:A.69, F:L.71, F:L.71, F:D.72, F:L.73, F:V.74, F:G.118, F:R.144 Salt bridges: F:K.31, F:R.32, F:R.32, F:H.66 pi-Stacking: B:F.255, B:F.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, D. et al., Crystal Structure of DmdD, a Crotonase Superfamily Enzyme That Catalyzes the Hydration and Hydrolysis of Methylthioacryloyl-CoA. Plos One (2013)

Release Date

2013-06-05

Peptides

Enoyl-CoA hydratase/isomerase family protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Enoyl-CoA hydratase/isomerase family protein

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