SMTL ID : 3s42.1

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x MLA: MALONIC ACID(Non-covalent)

MLA.1: 9 residues within 4Å: Chain A: H.167, K.194, A.196, M.227, M.229, R.237, F.249, A.257, Q.260 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.249 Hydrogen bonds: A:Q.260 Water bridges: A:R.106, A:R.106 Salt bridges: A:H.167, A:K.194, A:R.237 MLA.8: 10 residues within 4Å: Chain B: H.167, K.194, A.196, M.227, M.229, R.237, F.249, A.257, Q.260 Ligands: BO3.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.260 Salt bridges: B:H.167, B:K.194, B:R.237

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: E.241, V.242, L.273 Chain B: K.231, V.234 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.242 DMS.3: 5 residues within 4Å: Chain A: F.105, S.107, L.116, Y.121, E.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.116 Salt bridges: A:E.140 pi-Cation interactions: A:Y.121 DMS.4: 6 residues within 4Å: Chain A: K.109, E.110, H.167, D.168, F.169, H.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.168, A:F.169, A:H.170 DMS.7: 4 residues within 4Å: Chain A: K.231 Chain B: E.241, V.242, L.273 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.241 DMS.9: 7 residues within 4Å: Chain B: F.105, S.107, A.115, L.116, T.117, Y.121, E.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.116 DMS.10: 5 residues within 4Å: Chain B: K.26, E.217, R.218, Y.219, A.220 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.26

1 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 4 residues within 4Å: Chain A: H.2, H.4, H.158 Ligands: IMD.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.2, A:H.4, A:H.158

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.6: 4 residues within 4Å: Chain A: H.4, D.130, H.158 Ligands: NI.5 No protein-ligand interaction detected (PLIP)

1 x BO3: BORIC ACID(Non-covalent)

BO3.11: 8 residues within 4Å: Chain B: S.45, E.70, R.72, T.104, R.106, K.194, F.249 Ligands: MLA.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.45, B:E.70, B:R.72, B:R.106, B:R.106, B:K.194 Water bridges: B:R.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Light, S.H. et al., Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site. To be Published

Release Date

2011-06-01

Peptides

3-dehydroquinate dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

3-dehydroquinate dehydratase

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