SMTL ID : 2zy4.1

dodecameric L-aspartate beta-decarboxylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-12-mer

Ligands

12 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 16 residues within 4Å: Chain A: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 Chain B: Y.134 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.204, A:V.252, A:V.288, A:K.315 Hydrogen bonds: A:G.174, A:T.175, A:T.175, A:T.175, A:Y.207, A:N.256, A:Y.289, A:S.312, A:S.312, A:S.314 Water bridges: A:R.37, A:R.37 Salt bridges: A:R.37, A:K.315, A:R.323 pi-Cation interactions: A:R.37 PLP.3: 16 residues within 4Å: Chain A: Y.134 Chain B: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.37, B:F.204, B:V.252, B:V.288, B:K.315 Hydrogen bonds: B:G.174, B:T.175, B:T.175, B:N.256, B:Y.289, B:S.312, B:S.312, B:S.314, B:Y.441, A:Y.134 Salt bridges: B:R.37, B:K.315, B:R.323 pi-Cation interactions: B:R.37 PLP.5: 16 residues within 4Å: Chain C: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 Chain D: Y.134 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:R.37, C:F.204, C:V.252, C:V.288, C:K.315 Hydrogen bonds: C:G.174, C:T.175, C:T.175, C:N.256, C:S.312, C:S.312, C:S.314 Water bridges: C:Y.207 Salt bridges: C:R.37, C:K.315, C:R.323 pi-Cation interactions: C:R.37 PLP.7: 16 residues within 4Å: Chain C: Y.134 Chain D: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:R.37, D:F.204, D:V.252, D:K.315 Hydrogen bonds: D:G.174, D:T.175, D:T.175, D:T.175, D:Y.207, D:N.256, D:S.312, D:S.312, D:S.314, D:Y.441 Water bridges: D:R.37, D:R.37 Salt bridges: D:R.37, D:K.315, D:R.323 pi-Cation interactions: D:R.37 PLP.9: 16 residues within 4Å: Chain E: R.37, G.173, G.174, T.175, F.204, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323, Y.441 Chain K: Y.134 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:R.37, E:F.204, E:V.252, E:N.256, E:K.315 Hydrogen bonds: E:G.174, E:T.175, E:T.175, E:T.175, E:Y.207, E:N.256, E:Y.289, E:S.312, E:S.312, E:S.314, E:Y.441 Salt bridges: E:R.37, E:K.315, E:R.323 pi-Cation interactions: E:R.37 PLP.11: 16 residues within 4Å: Chain F: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 Chain L: Y.134 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:R.37, F:F.204, F:V.252, F:V.288, F:K.315 Hydrogen bonds: F:G.174, F:T.175, F:T.175, F:N.256, F:S.312, F:S.312, F:S.314 Water bridges: F:R.37, F:R.37 Salt bridges: F:R.37, F:K.315, F:R.323 PLP.13: 16 residues within 4Å: Chain G: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 Chain H: Y.134 18 PLIP interactions: 17 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:F.204, G:V.252, G:V.288, G:K.315 Hydrogen bonds: G:G.174, G:T.175, G:T.175, G:N.256, G:S.312, G:S.312, G:S.314, H:Y.134 Water bridges: G:R.37, G:R.37 Salt bridges: G:R.37, G:K.315, G:R.323 pi-Cation interactions: G:R.37 PLP.15: 16 residues within 4Å: Chain G: Y.134 Chain H: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 18 PLIP interactions: 18 interactions with chain H Hydrophobic interactions: H:R.37, H:F.204, H:V.252, H:V.288, H:K.315 Hydrogen bonds: H:G.174, H:T.175, H:T.175, H:T.175, H:Y.207, H:N.256, H:S.312, H:S.312, H:S.314 Salt bridges: H:R.37, H:K.315, H:R.323 pi-Cation interactions: H:R.37 PLP.17: 16 residues within 4Å: Chain I: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 Chain J: Y.134 21 PLIP interactions: 20 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:R.37, I:F.204, I:V.252, I:V.288, I:K.315 Hydrogen bonds: I:G.174, I:T.175, I:T.175, I:T.175, I:Y.207, I:N.256, I:Y.289, I:S.312, I:S.312, I:S.314, I:Y.441, J:Y.134 Salt bridges: I:R.37, I:K.315, I:R.323 pi-Cation interactions: I:R.37 PLP.19: 16 residues within 4Å: Chain I: Y.134 Chain J: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 19 PLIP interactions: 18 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:R.37, J:F.204, J:V.252, J:K.315 Hydrogen bonds: J:G.174, J:T.175, J:T.175, J:N.256, J:Y.289, J:S.312, J:S.312, J:S.314, I:Y.134 Water bridges: J:R.37, J:R.37 Salt bridges: J:R.37, J:K.315, J:R.323 pi-Cation interactions: J:R.37 PLP.21: 16 residues within 4Å: Chain E: Y.134 Chain K: R.37, G.173, G.174, T.175, F.204, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323, Y.441 17 PLIP interactions: 16 interactions with chain K, 1 interactions with chain E Hydrophobic interactions: K:R.37, K:F.204, K:V.252, K:N.256, K:K.315 Hydrogen bonds: K:G.174, K:T.175, K:T.175, K:N.256, K:S.312, K:S.312, K:S.314, E:Y.134 Salt bridges: K:R.37, K:K.315, K:R.323 pi-Cation interactions: K:R.37 PLP.23: 16 residues within 4Å: Chain F: Y.134 Chain L: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 21 PLIP interactions: 20 interactions with chain L, 1 interactions with chain F Hydrophobic interactions: L:R.37, L:F.204, L:V.252, L:V.288, L:K.315 Hydrogen bonds: L:G.174, L:T.175, L:T.175, L:T.175, L:Y.207, L:N.256, L:Y.289, L:S.312, L:S.312, L:S.314, F:Y.134 Water bridges: L:R.37, L:R.37 Salt bridges: L:R.37, L:K.315, L:R.323

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain B: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain C: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain D: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain E: R.49, R.53, E.98, G.99 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain F: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain G: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain H: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain I: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain J: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain K: R.49, R.53, E.98, G.99 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain L: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, H.-J. et al., Structure, Assembly, and Mechanism of a PLP-Dependent Dodecameric l-Aspartate beta-Decarboxylase. Structure (2009)

Release Date

2009-01-27

Peptides

L-aspartate beta-decarboxylase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

L-aspartate beta-decarboxylase

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