SMTL ID : 3ozy.1

Crystal structure of enolase superfamily member from Bordetella bronchiseptica complexed with Mg and m-Xylarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.171, K.173, D.201, E.227, E.254 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.201, A:E.227, A:E.254, H2O.18, H2O.19, H2O.19 MG.2: 2 residues within 4Å: Chain A: H.86, H.90 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.86, A:H.90, H2O.19, H2O.38 MG.8: 6 residues within 4Å: Chain B: K.171, K.173, D.201, E.227, E.254 Ligands: DXL.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.201, B:E.227, B:E.254, H2O.37 MG.9: 2 residues within 4Å: Chain B: H.86, H.90 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.86, B:H.90, H2O.18, H2O.32

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: D.57, W.375, E.378, P.379 Chain B: R.63, D.67, V.68, E.92 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.57, A:D.57, A:E.378, B:R.63, B:E.92 Water bridges: A:D.57, A:A.380, B:E.92, B:N.96 GOL.4: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.210, A:D.210 GOL.11: 8 residues within 4Å: Chain A: H.99, R.100, A.261, D.264 Chain B: R.100, L.256, A.261, D.264 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.99, A:R.100, A:R.100, A:D.264, B:R.100, B:R.100, B:D.264 GOL.12: 7 residues within 4Å: Chain A: R.63, D.67, V.68, E.92 Chain B: D.57, E.378, P.379 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.57, B:E.378, A:R.63, A:E.92 Water bridges: B:D.57, B:L.58, B:A.380, A:N.96

6 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 2 residues within 4Å: Chain A: G.207, R.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.208 Water bridges: A:H.209 ACY.6: 5 residues within 4Å: Chain A: W.148, D.149, R.176, A.177, D.181 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.149, A:A.177 Water bridges: A:L.150, A:R.176 Salt bridges: A:R.176 ACY.7: 7 residues within 4Å: Chain A: S.25, A.27, K.30, Y.147, K.173, N.203, F.306 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.27 Hydrogen bonds: A:S.25, A:Y.147, A:N.203 Water bridges: A:S.25, A:K.30, A:K.173, A:K.173, A:K.173, A:K.173 Salt bridges: A:K.30, A:K.173 ACY.13: 2 residues within 4Å: Chain B: R.22, P.379 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.379 Water bridges: B:R.22, B:R.22, B:N.32, B:N.32 Salt bridges: B:R.22 ACY.14: 1 residues within 4Å: Chain B: H.298 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.300 ACY.15: 6 residues within 4Å: Chain B: W.148, D.149, R.176, A.177, K.180, D.181 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.180 Hydrogen bonds: B:D.149, B:A.177 Water bridges: B:W.148, B:A.177 Salt bridges: B:R.176

1 x DXL: D-xylaric acid(Non-covalent)

DXL.10: 15 residues within 4Å: Chain B: S.25, A.27, K.30, S.144, Y.147, K.171, K.173, D.201, N.203, E.227, E.254, H.304, F.306, E.329 Ligands: MG.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.25, B:K.30, B:S.144, B:K.173, B:N.203 Water bridges: B:S.25, B:Y.147, B:H.304, B:F.306 Salt bridges: B:K.30, B:K.171, B:K.173, B:K.173, B:H.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of enolase superfamily member from Bordetella bronchiseptica complexed with Mg and m-Xylarate. To be Published

Release Date

2011-09-28

Peptides

Putative mandelate racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative mandelate racemase

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