SMTL ID : 6cv6.2 (3 other biounits)

Crystal structure of 3-dehydroquinate dehydratase, type II, from Burkholderia phymatum STM815

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

6 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 8 residues within 4Å: Chain A: Y.103, R.106, H.133, S.134, V.135, E.138 Chain B: E.128, F.130 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.103, A:H.133 Water bridges: A:R.106, A:R.106 Salt bridges: A:R.106, A:H.133 TLA.2: 13 residues within 4Å: Chain A: H.31, R.37, Y.42, N.94, G.96, A.97, H.100, H.120, M.121, S.122, R.127, R.131 Chain C: D.107 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.42, A:N.94, A:G.96, A:H.100, A:H.120, A:M.121, A:S.122, A:S.122, A:R.127, A:R.131, C:D.107 Water bridges: A:R.37 Salt bridges: A:H.31, A:R.37, A:H.120 TLA.4: 8 residues within 4Å: Chain B: Y.103, R.106, H.133, S.134, V.135, E.138 Chain C: E.128, F.130 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.106, B:H.133, B:V.135 Salt bridges: B:R.106, B:H.133 TLA.5: 12 residues within 4Å: Chain A: D.107 Chain B: H.31, R.37, Y.42, N.94, G.96, A.97, H.120, M.121, S.122, R.127, R.131 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.94, B:G.96, B:A.97, B:M.121, B:S.122, B:S.122, B:R.127, B:R.131, A:D.107 Salt bridges: B:H.31, B:R.37, B:H.120 TLA.7: 7 residues within 4Å: Chain A: F.130 Chain C: Y.103, R.106, H.133, S.134, V.135, E.138 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.103, C:H.133 Salt bridges: C:R.106, C:H.133 Water bridges: A:F.130 TLA.8: 9 residues within 4Å: Chain C: H.31, N.94, G.96, H.120, M.121, S.122, V.124, R.127, R.131 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.94, C:M.121, C:S.122, C:S.122, C:R.127, C:R.131 Water bridges: C:A.97, C:R.127 Salt bridges: C:H.120, C:H.120

3 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.3: 3 residues within 4Å: Chain A: H.125, H.132, H.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.125 Water bridges: A:S.134, A:S.134 Salt bridges: A:H.132, A:H.133 TAR.6: 3 residues within 4Å: Chain B: H.125, H.132, H.133 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.125 Water bridges: B:S.134, B:S.137 Salt bridges: B:H.132, B:H.133 TAR.9: 3 residues within 4Å: Chain C: H.125, H.132, H.133 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.125 Water bridges: C:S.134, C:S.137 Salt bridges: C:H.132, C:H.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of 3-dehydroquinate dehydratase, type II, from Burkholderia phymatum STM815. to be published

Release Date

2018-04-11

Peptides

3-dehydroquinate dehydratase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
F

3-dehydroquinate dehydratase

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