SMTL ID : 4j7h.3 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-tetramer

Ligands

4 x TLO: 5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHENOXY)PHOSPHORYL]OXY}PHOSPHORYL]THYMIDINE(Non-covalent)

TLO.1: 14 residues within 4Å: Chain A: W.67, H.78, F.83, F.84, G.117, Q.153, A.154, T.155, N.158, N.200, W.320, T.321, Q.322, R.408 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.83, A:F.84, A:T.155, A:W.320, A:Q.322 Hydrogen bonds: A:Q.153, A:N.158, A:T.321 Water bridges: A:T.155 Salt bridges: A:R.408 pi-Stacking: A:F.83, A:W.320 TLO.7: 14 residues within 4Å: Chain B: W.67, H.78, F.83, F.84, G.117, Q.153, A.154, T.155, N.158, N.200, W.320, T.321, Q.322, R.408 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.83, B:F.84, B:T.155, B:W.320, B:Q.322 Hydrogen bonds: B:Q.153, B:N.158, B:T.321 Water bridges: B:T.155 Salt bridges: B:R.408 pi-Stacking: B:F.83, B:W.320 TLO.13: 14 residues within 4Å: Chain C: W.67, H.78, F.83, F.84, G.117, Q.153, A.154, T.155, N.158, N.200, W.320, T.321, Q.322, R.408 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.83, C:F.84, C:T.155, C:W.320, C:Q.322 Hydrogen bonds: C:Q.153, C:N.158, C:T.321 Water bridges: C:T.155, C:R.408, C:R.408 Salt bridges: C:R.408 pi-Stacking: C:F.83, C:W.320 TLO.17: 14 residues within 4Å: Chain D: W.67, H.78, F.83, F.84, G.117, Q.153, A.154, T.155, N.158, N.200, W.320, T.321, Q.322, R.408 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.83, D:F.84, D:T.155, D:W.320, D:Q.322 Hydrogen bonds: D:Q.153, D:N.158, D:T.321 Water bridges: D:T.155, D:R.408, D:R.408 Salt bridges: D:R.408 pi-Stacking: D:F.83, D:W.320

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

TRH.2: 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:Q.108, A:Y.302, A:F.303, A:V.333, A:Q.367 Hydrogen bonds: A:R.104, A:S.193, A:S.193, A:R.351, A:Q.367, A:T.369, A:T.369, A:N.372 Water bridges: A:Q.191, A:S.193, A:S.193, A:H.297, A:R.351, A:R.351, A:D.353, A:Y.373, A:Y.373, A:E.452 Salt bridges: A:R.351, A:R.351 pi-Stacking: A:W.106, A:Y.302 TRH.8: 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:Q.108, B:Y.302, B:F.303, B:V.333, B:Q.367 Hydrogen bonds: B:R.104, B:S.193, B:S.193, B:R.351, B:Q.367, B:T.369, B:T.369, B:N.372 Water bridges: B:Q.191, B:S.193, B:S.193, B:H.297, B:R.351, B:R.351, B:D.353, B:Y.373, B:Y.373, B:E.452 Salt bridges: B:R.351, B:R.351 pi-Stacking: B:W.106, B:Y.302 TRH.14: 18 residues within 4Å: Chain C: 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, E.452 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:W.106, C:Q.108, C:Y.302, C:F.303, C:V.333, C:Q.367 Hydrogen bonds: C:R.104, C:S.193, C:S.193, C:Y.302, C:R.351, C:D.353, C:Q.367, C:T.369, C:T.369, C:T.369, C:N.372, C:Y.373 Water bridges: C:S.193, C:S.193, C:H.297, C:D.353, C:Y.373, C:E.452, C:E.452 Salt bridges: C:R.351, C:R.351 pi-Stacking: C:W.106, C:Y.302 TRH.18: 18 residues within 4Å: Chain D: 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, E.452 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:W.106, D:Q.108, D:Y.302, D:F.303, D:V.333, D:Q.367 Hydrogen bonds: D:R.104, D:S.193, D:S.193, D:Y.302, D:R.351, D:D.353, D:Q.367, D:T.369, D:T.369, D:T.369, D:N.372, D:Y.373 Water bridges: D:S.193, D:S.193, D:H.297, D:D.353, D:Y.373, D:E.452, D:E.452 Salt bridges: D:R.351, D:R.351 pi-Stacking: D:W.106, D:Y.302

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: R.276 Chain B: R.112, R.279 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.112, B:R.112, B:R.279, A:R.276 Water bridges: A:H.94 EDO.4: 4 residues within 4Å: Chain A: A.391, R.393, I.396, R.415 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.393, A:R.415 Water bridges: A:A.391 EDO.5: 8 residues within 4Å: Chain A: L.387, A.391, P.392, R.395, I.419, D.420, A.421, D.422 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.395, A:D.422 EDO.6: 3 residues within 4Å: Chain A: V.337, P.344, I.460 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: R.112, R.279 Chain B: R.276 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.276, A:R.112, A:R.112, A:R.279 Water bridges: B:H.94 EDO.10: 4 residues within 4Å: Chain B: A.391, R.393, I.396, R.415 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.393, B:R.415 Water bridges: B:A.391 EDO.11: 8 residues within 4Å: Chain B: L.387, A.391, P.392, R.395, I.419, D.420, A.421, D.422 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.395, B:D.422 EDO.12: 3 residues within 4Å: Chain B: V.337, P.344, I.460 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain C: R.276 Chain D: R.112, R.279 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.276, D:R.112, D:R.112 Water bridges: C:V.277 EDO.16: 7 residues within 4Å: Chain C: L.387, R.395, I.419, D.420, A.421, D.422, I.425 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.395, C:R.395, C:D.422 EDO.19: 3 residues within 4Å: Chain C: R.112, R.279 Chain D: R.276 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.276, C:R.112, C:R.112 Water bridges: D:V.277 EDO.20: 7 residues within 4Å: Chain D: L.387, R.395, I.419, D.420, A.421, D.422, I.425 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.395, D:R.395, D:D.422

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

EvaA 2,3-dehydratase

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