SMTL ID : 3ozm.5 (4 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: K.171, K.173, D.201, E.227, E.254 Ligands: DXL.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.201, A:E.227, A:E.254, H2O.12 MG.4: 6 residues within 4Å: Chain B: K.171, K.173, D.201, E.227, E.254 Ligands: DXL.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.201, B:E.227, B:E.254, H2O.24 MG.8: 6 residues within 4Å: Chain C: K.171, K.173, D.201, E.227, E.254 Ligands: DXL.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.201, C:E.227, C:E.254, H2O.35 MG.13: 5 residues within 4Å: Chain D: K.171, D.201, E.227, E.254 Ligands: LY9.14 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.201, D:E.227, D:E.254, H2O.47 MG.16: 6 residues within 4Å: Chain E: K.171, K.173, D.201, E.227, E.254 Ligands: DXL.17 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.201, E:E.227, E:E.254, H2O.57 MG.19: 6 residues within 4Å: Chain F: K.171, K.173, D.201, E.227, E.254 Ligands: DXL.20 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.201, F:E.227, F:E.254, H2O.58 MG.21: 6 residues within 4Å: Chain G: K.171, K.173, D.201, E.227, E.254 Ligands: DXL.22 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.201, G:E.227, G:E.254, H2O.80 MG.24: 5 residues within 4Å: Chain H: K.171, D.201, E.227, E.254 Ligands: LY9.25 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.201, H:E.227, H:E.254, H2O.89

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

DXL.2: 15 residues within 4Å: Chain A: 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.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.25, A:K.30, A:K.30, A:S.144, A:Y.147, A:N.203 Water bridges: A:S.25, A:Y.142, A:K.173, A:F.306, A:E.329 Salt bridges: A:K.30, A:K.171, A:K.173, A:K.173, A:H.304 DXL.5: 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.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.25, B:K.30, B:S.144, B:N.203 Water bridges: B:S.25, B:Y.142, B:F.306, B:E.329 Salt bridges: B:K.30, B:K.171, B:K.173, B:K.173, B:H.304 DXL.9: 15 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:S.25, C:K.30, C:S.144, C:Y.147, C:N.203 Water bridges: C:S.25, C:Y.142, C:K.173, C:F.306 Salt bridges: C:K.30, C:K.171, C:K.173, C:K.173, C:H.304 DXL.17: 15 residues within 4Å: Chain E: 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.16 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:S.25, E:K.30, E:K.30, E:S.144, E:N.203 Water bridges: E:S.25, E:Y.142, E:K.173, E:K.173, E:E.227, E:F.306 Salt bridges: E:K.30, E:K.171, E:K.173, E:K.173, E:H.304 DXL.20: 14 residues within 4Å: Chain F: S.25, A.27, K.30, Y.147, K.171, K.173, D.201, N.203, E.227, E.254, H.304, F.306, E.329 Ligands: MG.19 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:S.25, F:K.30, F:S.144, F:Y.147, F:D.201, F:N.203 Water bridges: F:S.25, F:K.30, F:Y.142, F:K.173, F:F.306 Salt bridges: F:K.30, F:K.171, F:K.173, F:K.173, F:H.304 DXL.22: 14 residues within 4Å: Chain G: S.25, A.27, K.30, Y.147, K.171, K.173, D.201, N.203, E.227, E.254, H.304, F.306, E.329 Ligands: MG.21 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:S.25, G:K.30, G:K.30, G:S.144, G:N.203 Water bridges: G:S.25, G:E.227, G:F.306, G:E.329 Salt bridges: G:K.30, G:K.171, G:K.173, G:K.173, G:H.304

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: T.47, V.49, R.120, E.364, I.365, W.367 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.47, A:E.364, A:I.365, A:W.367 Water bridges: A:T.47 GOL.6: 7 residues within 4Å: Chain B: W.85, H.86, F.89, H.90, R.259, N.260, E.286 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain H Hydrogen bonds: B:H.90, B:R.259, B:N.260 Water bridges: H:D.233 GOL.7: 5 residues within 4Å: Chain B: R.63, D.67, V.68, E.92 Chain H: D.57 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain B Hydrogen bonds: H:D.57, B:R.63, B:E.92 Water bridges: H:L.58 GOL.10: 7 residues within 4Å: Chain C: E.197, G.222, C.223, Y.224, P.247, V.248, R.249 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.197, C:P.247, C:R.249 Water bridges: C:D.219, C:R.249 GOL.11: 5 residues within 4Å: Chain C: D.57, E.378 Chain E: R.63, D.67, E.92 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain C Hydrogen bonds: E:R.63, E:E.92, C:D.57, C:D.57, C:E.378 Water bridges: E:N.96, C:D.57, C:L.58, C:A.380 GOL.12: 5 residues within 4Å: Chain C: D.67, V.68, E.92 Chain E: D.57, I.381 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:D.57, E:I.381, C:D.67 Water bridges: E:D.57, E:L.58, E:I.381 GOL.15: 7 residues within 4Å: Chain D: E.197, G.222, C.223, Y.224, P.247, V.248, R.249 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.197, D:C.223, D:P.247, D:R.249 Water bridges: D:R.249, D:R.249 GOL.18: 6 residues within 4Å: Chain E: T.47, V.49, R.120, E.364, I.365, W.367 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:T.47, E:F.363, E:E.364, E:I.365, E:W.367 Water bridges: E:T.47 GOL.23: 7 residues within 4Å: Chain G: W.85, H.86, F.89, H.90, R.259, N.260, E.286 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:H.86, G:H.90, G:R.259, G:N.260 Water bridges: A:S.231 GOL.26: 7 residues within 4Å: Chain H: E.197, G.222, C.223, Y.224, P.247, V.248, R.249 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:E.197, H:P.247, H:R.249 Water bridges: H:R.249

2 x LY9: L-arabinaric acid(Non-covalent)

LY9.14: 10 residues within 4Å: Chain D: K.171, K.173, D.201, N.203, E.227, E.254, H.304, F.306, E.329 Ligands: MG.13 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:K.173, D:K.173, D:N.203 Water bridges: D:E.329, D:E.329 Salt bridges: D:K.171, D:K.173, D:H.304 LY9.25: 11 residues within 4Å: Chain H: K.30, K.171, K.173, D.201, N.203, E.227, E.254, H.304, F.306, E.329 Ligands: MG.24 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:K.173, H:K.173, H:N.203 Water bridges: H:Y.142 Salt bridges: H:K.30, H:K.171, H:K.173, H: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, m-Xylarate and L-Lyxarate. TO BE PUBLISHED

Release Date

2011-09-28

Peptides

Putative mandelate racemase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Putative mandelate racemase

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