SMTL ID : 7a8y.1

X-ray crystal structure of Aspartate alpha-decarboxylase in complex with D-Serine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-4-4-mer

Ligands

6 x DSN: D-SERINE(Covalent)(Non-covalent)(Non-functional Binders)

DSN.1: 9 residues within 4Å: Chain A: Y.25 Chain B: S.1, Y.34, N.48, G.49 Chain G: K.12, H.14 Chain H: I.62 Ligands: DSN.2 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain G Hydrophobic interactions: B:Y.34 Hydrogen bonds: B:S.1, B:S.1, B:Y.34, B:Y.34 Salt bridges: G:K.12, G:H.14 DSN.2: 11 residues within 4Å: Chain B: S.1, T.33, N.48, G.49, A.50, A.51 Chain G: K.12 Chain H: W.23, R.30, I.62 Ligands: DSN.1 9 PLIP interactions: 7 interactions with chain B, 1 interactions with chain H, 1 interactions with chain G Hydrogen bonds: B:S.1, B:T.33, B:T.33, B:Y.34, B:Y.34, B:A.50, B:A.51, G:K.12 Salt bridges: H:R.30 DSN.5: 9 residues within 4Å: Chain A: K.12, H.14 Chain B: I.62 Chain C: Y.25, G.27 Chain D: S.1, Y.34, N.48 Ligands: SER.4 6 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: D:S.1, D:Y.34, A:K.12 Hydrophobic interactions: B:I.62 Salt bridges: A:K.12, A:H.14 DSN.6: 9 residues within 4Å: Chain C: K.12, H.14 Chain D: I.62 Chain E: Y.25 Chain F: S.1, Y.34, N.48, G.49 Ligands: DSN.7 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: F:Y.34 Hydrogen bonds: F:S.1, F:S.1, F:Y.34 Salt bridges: C:K.12, C:H.14 DSN.7: 11 residues within 4Å: Chain C: K.12 Chain D: W.23, R.30, I.62 Chain F: S.1, T.33, N.48, G.49, A.50, A.51 Ligands: DSN.6 8 PLIP interactions: 6 interactions with chain F, 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: F:S.1, F:T.33, F:T.33, F:Y.34, F:A.50, F:A.51, C:K.12 Salt bridges: D:R.30 DSN.10: 9 residues within 4Å: Chain E: K.12, H.14 Chain F: I.62 Chain G: Y.25, G.27 Chain H: S.1, Y.34, N.48 Ligands: SER.9 7 PLIP interactions: 3 interactions with chain E, 3 interactions with chain H, 1 interactions with chain F Hydrogen bonds: E:K.12, H:S.1, H:Y.34, H:Y.34 Salt bridges: E:K.12, E:H.14 Hydrophobic interactions: F:I.62

2 x EDO: 1,2-ETHANEDIOL(Non-covalent)(Covalent)

EDO.3: 5 residues within 4Å: Chain D: Q.6, L.9, D.10, I.14, L.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.10, D:I.14 Water bridges: D:E.16 EDO.8: 5 residues within 4Å: Chain H: Q.6, L.9, D.10, I.14, L.15 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:I.14 Water bridges: H:E.16

2 x SER: SERINE(Covalent)(Non-covalent)

SER.4: 10 residues within 4Å: Chain B: W.23, R.30, I.62 Chain D: S.1, T.33, N.48, G.49, A.50, A.51 Ligands: DSN.5 8 PLIP interactions: 3 interactions with chain D, 4 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: D:S.1, D:A.50, D:A.51, S.4, S.4, S.4, S.4 Salt bridges: B:R.30 SER.9: 10 residues within 4Å: Chain F: W.23, R.30, I.62 Chain H: S.1, T.33, N.48, G.49, A.50, A.51 Ligands: DSN.10 9 PLIP interactions: 4 interactions with chain H, 1 interactions with chain F, 4 Ligand-Ligand interactions Hydrogen bonds: H:S.1, H:T.33, H:A.50, H:A.51, S.9, S.9, S.9, S.9 Salt bridges: F:R.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raskar, T. et al., Structure and diffusive dynamics of aspartate alpha-decarboxylase (ADC) liganded with D-serine in aqueous solution. Phys Chem Chem Phys (2022)

Release Date

2021-10-06

Peptides

Aspartate 1-decarboxylase: ACEG
Aspartate 1-decarboxylase: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

C
DDD

E
AAA

G
DDD

B
BBB

D
EaE

F
BBB

H
EaE

Aspartate 1-decarboxylase

Aspartate 1-decarboxylase