SMTL ID : 2p8c.1

Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579 complexed with N-succinyl Arg.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: K.161, D.191, N.193, E.218, D.243 Ligands: SUG.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.191, A:E.218, A:D.243, H2O.1, SUG.2 MG.3: 6 residues within 4Å: Chain B: K.161, D.191, N.193, E.218, D.243 Ligands: SUG.4 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.191, B:E.218, B:D.243, SUG.4, H2O.7 MG.5: 6 residues within 4Å: Chain C: K.161, D.191, N.193, E.218, D.243 Ligands: SUG.6 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:D.191, C:E.218, C:D.243, SUG.6, H2O.13 MG.7: 6 residues within 4Å: Chain D: K.161, D.191, N.193, E.218, D.243 Ligands: SUG.8 5 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: D:D.191, D:E.218, D:D.243, SUG.8, H2O.20 MG.9: 6 residues within 4Å: Chain E: K.161, D.191, N.193, E.218, D.243 Ligands: SUG.10 5 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: E:D.191, E:E.218, E:D.243, SUG.10, H2O.26 MG.11: 6 residues within 4Å: Chain F: K.161, D.191, N.193, E.218, D.243 Ligands: SUG.12 5 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: F:D.191, F:E.218, F:D.243, SUG.12, H2O.32 MG.13: 6 residues within 4Å: Chain G: K.161, D.191, N.193, E.218, D.243 Ligands: SUG.14 5 PLIP interactions: 3 interactions with chain G, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: G:D.191, G:E.218, G:D.243, SUG.14, H2O.39 MG.15: 6 residues within 4Å: Chain H: K.161, D.191, N.193, E.218, D.243 Ligands: SUG.16 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.191, H:E.218, H:D.243, H2O.45

8 x SUG: N~2~-(3-CARBOXYPROPANOYL)-L-ARGININE(Non-covalent)

SUG.2: 21 residues within 4Å: Chain A: F.19, Y.26, M.29, V.49, D.51, V.136, K.161, K.163, D.191, N.193, E.218, D.243, K.267, S.295, M.296, V.297, E.320, L.321, T.322, G.323 Ligands: MG.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.19, A:V.136, A:V.297 Hydrogen bonds: A:K.161, A:K.163, A:N.193, A:N.265, A:K.267, A:S.295, A:S.295, A:M.296, A:T.322, A:G.323 Water bridges: A:Y.26, A:D.51, A:N.193, A:N.193, A:E.244, A:S.295, A:S.295 Salt bridges: A:D.51, A:K.161, A:K.163, A:K.267 pi-Cation interactions: A:Y.26 SUG.4: 21 residues within 4Å: Chain B: F.19, Y.26, M.29, V.49, D.51, V.136, K.161, K.163, D.191, N.193, E.218, D.243, K.267, S.295, M.296, V.297, E.320, L.321, T.322, G.323 Ligands: MG.3 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:F.19, B:V.136, B:V.297 Hydrogen bonds: B:K.161, B:K.163, B:N.193, B:N.265, B:K.267, B:S.295, B:S.295, B:M.296, B:T.322, B:G.323 Water bridges: B:Y.26, B:D.51, B:N.193, B:N.193, B:E.244, B:S.295, B:S.295 Salt bridges: B:D.51, B:K.161, B:K.163, B:K.267 pi-Cation interactions: B:Y.26 SUG.6: 21 residues within 4Å: Chain C: F.19, Y.26, M.29, V.49, D.51, V.136, K.161, K.163, D.191, N.193, E.218, D.243, K.267, S.295, M.296, V.297, E.320, L.321, T.322, G.323 Ligands: MG.5 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:F.19, C:V.136, C:V.297 Hydrogen bonds: C:K.161, C:K.163, C:N.193, C:N.265, C:K.267, C:S.295, C:S.295, C:M.296, C:T.322, C:G.323 Water bridges: C:Y.26, C:D.51, C:N.193, C:N.193, C:E.244, C:S.295, C:S.295 Salt bridges: C:D.51, C:K.161, C:K.163, C:K.267 pi-Cation interactions: C:Y.26 SUG.8: 21 residues within 4Å: Chain D: F.19, Y.26, M.29, V.49, D.51, V.136, K.161, K.163, D.191, N.193, E.218, D.243, K.267, S.295, M.296, V.297, E.320, L.321, T.322, G.323 Ligands: MG.7 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:F.19, D:V.136, D:V.297 Hydrogen bonds: D:K.161, D:K.163, D:N.193, D:N.265, D:K.267, D:S.295, D:S.295, D:M.296, D:T.322, D:G.323 Water bridges: D:Y.26, D:D.51, D:N.193, D:N.193, D:E.244, D:S.295, D:S.295 Salt bridges: D:D.51, D:K.161, D:K.163, D:K.267 pi-Cation interactions: D:Y.26 SUG.10: 21 residues within 4Å: Chain E: F.19, Y.26, M.29, V.49, D.51, V.136, K.161, K.163, D.191, N.193, E.218, D.243, K.267, S.295, M.296, V.297, E.320, L.321, T.322, G.323 Ligands: MG.9 26 PLIP interactions: 26 interactions with chain E Hydrophobic interactions: E:F.19, E:V.136, E:V.297 Hydrogen bonds: E:K.161, E:K.163, E:N.193, E:N.265, E:K.267, E:S.295, E:S.295, E:M.296, E:T.322, E:G.323 Water bridges: E:Y.26, E:D.51, E:N.193, E:N.193, E:E.244, E:S.295, E:E.320, E:E.320 Salt bridges: E:D.51, E:K.161, E:K.163, E:K.267 pi-Cation interactions: E:Y.26 SUG.12: 21 residues within 4Å: Chain F: F.19, Y.26, M.29, V.49, D.51, V.136, K.161, K.163, D.191, N.193, E.218, D.243, K.267, S.295, M.296, V.297, E.320, L.321, T.322, G.323 Ligands: MG.11 26 PLIP interactions: 26 interactions with chain F Hydrophobic interactions: F:F.19, F:V.136, F:V.297 Hydrogen bonds: F:K.161, F:K.163, F:N.193, F:N.265, F:K.267, F:S.295, F:S.295, F:M.296, F:T.322, F:G.323 Water bridges: F:Y.26, F:D.51, F:N.193, F:N.193, F:E.244, F:S.295, F:E.320, F:E.320 Salt bridges: F:D.51, F:K.161, F:K.163, F:K.267 pi-Cation interactions: F:Y.26 SUG.14: 21 residues within 4Å: Chain G: F.19, Y.26, M.29, V.49, D.51, V.136, K.161, K.163, D.191, N.193, E.218, D.243, K.267, S.295, M.296, V.297, E.320, L.321, T.322, G.323 Ligands: MG.13 26 PLIP interactions: 26 interactions with chain G Hydrophobic interactions: G:F.19, G:V.136, G:V.297 Hydrogen bonds: G:K.161, G:K.163, G:N.193, G:N.265, G:K.267, G:S.295, G:S.295, G:M.296, G:T.322, G:G.323 Water bridges: G:Y.26, G:D.51, G:N.193, G:N.193, G:E.244, G:S.295, G:E.320, G:E.320 Salt bridges: G:D.51, G:K.161, G:K.163, G:K.267 pi-Cation interactions: G:Y.26 SUG.16: 21 residues within 4Å: Chain H: F.19, Y.26, M.29, V.49, D.51, V.136, K.161, K.163, D.191, N.193, E.218, D.243, K.267, S.295, M.296, V.297, E.320, L.321, T.322, G.323 Ligands: MG.15 26 PLIP interactions: 26 interactions with chain H Hydrophobic interactions: H:F.19, H:V.136, H:V.297 Hydrogen bonds: H:K.161, H:K.163, H:N.193, H:N.265, H:K.267, H:S.295, H:S.295, H:M.296, H:T.322, H:G.323 Water bridges: H:Y.26, H:D.51, H:N.193, H:N.193, H:E.244, H:S.295, H:E.320, H:E.320 Salt bridges: H:D.51, H:K.161, H:K.163, H:K.267 pi-Cation interactions: H:Y.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, L. et al., Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat.Chem.Biol. (2007)

Release Date

2007-07-03

Peptides

Mandelate racemase/muconate lactonizing enzyme family protein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Mandelate racemase/muconate lactonizing enzyme family protein

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