SMTL ID : 5kaj.3 (3 other biounits)

Crystal structure of a dioxygenase in the Crotonase superfamily in P21, A319C mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-trimer

Ligands

3 x YE2: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[(~{E})-2-[3,5-bis(oxidanyl)phenyl]-1-oxidanyl-ethenyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate(Non-covalent)

YE2.1: 30 residues within 4Å: Chain A: R.185, L.186, A.188, E.189, H.222, R.224, Y.225, A.233, G.234, I.235, N.236, L.237, K.238, F.250, L.251, R.254, F.292, I.294, G.295, G.296, Q.299, Y.314, P.318, C.319, E.322, I.324, I.325, G.327, F.412, Q.416 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.235, A:I.235, A:L.251, A:F.292, A:I.294, A:I.324 Hydrogen bonds: A:E.189, A:A.233, A:I.235, A:I.235, A:L.237, A:K.238, A:G.296, A:I.325, A:G.327, A:Q.416 Salt bridges: A:H.222, A:H.222, A:R.224, A:R.224, A:K.238 YE2.2: 29 residues within 4Å: Chain B: R.185, L.186, A.188, E.189, H.222, R.224, Y.225, A.233, G.234, I.235, N.236, L.237, K.238, F.250, L.251, R.254, F.292, I.294, G.295, G.296, Q.299, Y.314, P.318, C.319, I.324, I.325, G.327, F.412, Q.416 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.235, B:I.235, B:L.251, B:F.292, B:I.294, B:I.324 Hydrogen bonds: B:E.189, B:Y.225, B:A.233, B:I.235, B:I.235, B:L.237, B:G.296, B:I.325, B:G.327, B:Q.416 Water bridges: B:R.254 Salt bridges: B:H.222 YE2.3: 27 residues within 4Å: Chain C: R.185, L.186, A.188, E.189, H.222, R.224, Y.225, A.233, G.234, I.235, N.236, L.237, K.238, F.250, L.251, R.254, F.292, I.294, G.295, G.296, Q.299, Y.314, P.318, C.319, I.325, G.327, Q.416 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.235, C:I.235, C:F.250, C:L.251, C:F.292, C:I.294, C:I.294 Hydrogen bonds: C:E.189, C:A.233, C:I.235, C:I.235, C:L.237, C:K.238, C:G.296, C:I.325, C:G.327, C:Q.416 Water bridges: C:E.255 Salt bridges: C:H.222, C:H.222, C:K.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, K. et al., Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase. Acta Crystallogr D Struct Biol (2017)

Release Date

2017-06-21

Peptides

(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase

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