SMTL ID : 4j7g.1 (2 other biounits)

Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-fucose and dTDP-rhamnose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x TRH: 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE(Non-covalent)

TRH.1: 17 residues within 4Å: Chain A: R.104, W.106, Q.107, Q.108, S.193, W.194, W.288, H.297, Y.302, F.303, V.333, R.351, Q.367, C.368, T.369, N.372, Y.373 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:W.106, A:Y.302, A:F.303, A:V.333, A:Q.367 Hydrogen bonds: A:R.104, A:S.193, A:W.194, A:Y.302, A:R.351, A:Q.367, A:T.369, A:T.369, A:T.369, A:N.372, A:Y.373 Water bridges: A:Q.191, A:S.193, A:S.193, A:H.297, A:R.351, A:D.353, A:Y.373, A:E.452 Salt bridges: A:R.351, A:R.351 pi-Stacking: A:W.106, A:Y.302 TRH.3: 17 residues within 4Å: Chain B: R.104, W.106, Q.107, Q.108, S.193, W.194, W.288, H.297, Y.302, F.303, V.333, R.351, Q.367, C.368, T.369, N.372, Y.373 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:W.106, B:Y.302, B:F.303, B:V.333, B:Q.367 Hydrogen bonds: B:R.104, B:S.193, B:W.194, B:Y.302, B:R.351, B:Q.367, B:T.369, B:T.369, B:T.369, B:N.372, B:Y.373 Water bridges: B:Q.191, B:S.193, B:S.193, B:H.297, B:R.351, B:D.353, B:Y.373, B:E.452 Salt bridges: B:R.351, B:R.351 pi-Stacking: B:W.106, B:Y.302

2 x 1JB: [[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2R,3R,4S,5R,6R)-6-METHYL-3,4,5-TRIS(OXIDANYL)OXAN-2-YL] HYDROGEN PHOSPHATE(Non-covalent)

1JB.2: 19 residues within 4Å: Chain A: W.67, H.78, F.83, G.117, I.118, L.119, Q.153, A.154, T.155, N.158, Y.159, N.200, N.238, W.320, T.321, Q.322, E.405, G.407, R.408 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.83, A:L.119, A:W.320 Hydrogen bonds: A:T.155, A:T.155, A:T.155, A:N.158, A:Y.159, A:N.200, A:N.238, A:E.405, A:R.408 Water bridges: A:H.78, A:Q.153, A:Q.153, A:K.198, A:T.321, A:Q.322, A:G.407 Salt bridges: A:R.408, A:R.408 pi-Stacking: A:F.83, A:W.320 1JB.4: 19 residues within 4Å: Chain B: W.67, H.78, F.83, G.117, I.118, L.119, Q.153, A.154, T.155, N.158, Y.159, N.200, N.238, W.320, T.321, Q.322, E.405, G.407, R.408 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:F.83, B:L.119, B:W.320 Hydrogen bonds: B:T.155, B:T.155, B:T.155, B:N.158, B:Y.159, B:N.200, B:N.238, B:E.405, B:R.408 Water bridges: B:H.78, B:Q.153, B:Q.153, B:K.198, B:T.321, B:Q.322, B:G.407 Salt bridges: B:R.408, B:R.408 pi-Stacking: B:F.83, B:W.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubiak, R.L. et al., Structure of EvaA: A Paradigm for Sugar 2,3-Dehydratases. Biochemistry (2013)

Release Date

2013-05-22

Peptides

EvaA 2,3-dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

EvaA 2,3-dehydratase

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