SMTL ID : 7ae5.1

Structure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in open form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

hetero-6-6-mer

Ligands

12 x RB: RUBIDIUM ION(Non-covalent)

RB.1: 4 residues within 4Å: Chain A: R.407, D.413, D.441, T.443 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.407, A:D.413, A:D.441, A:T.443, H2O.3 RB.2: 5 residues within 4Å: Chain A: V.164, M.216, T.219, Y.223, E.227 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.216, A:T.219, A:Y.223, A:E.227, H2O.3 RB.3: 4 residues within 4Å: Chain B: R.407, D.413, D.441, T.443 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.413, B:D.441, B:T.443, H2O.6, H2O.8 RB.4: 6 residues within 4Å: Chain B: V.164, M.216, A.217, T.219, Y.223, E.227 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:V.164, B:M.216, B:T.219, B:Y.223, B:E.227 RB.5: 4 residues within 4Å: Chain C: R.407, D.413, D.441, T.443 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:R.407, C:D.413, C:D.441, C:T.443, H2O.12 RB.6: 6 residues within 4Å: Chain C: V.164, M.216, A.217, T.219, Y.223, E.227 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:V.164, C:M.216, C:T.219, C:Y.223, C:E.227 RB.7: 4 residues within 4Å: Chain D: R.407, D.413, D.441, T.443 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:R.407, D:D.413, D:D.441, D:T.443, H2O.19 RB.8: 6 residues within 4Å: Chain D: V.164, M.216, A.217, T.219, Y.223, E.227 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:V.164, D:M.216, D:T.219, D:Y.223, H2O.16 RB.9: 4 residues within 4Å: Chain E: R.407, D.413, D.441, T.443 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.413, E:D.413, E:D.441, E:T.443, H2O.23 RB.10: 6 residues within 4Å: Chain E: V.164, M.216, A.217, T.219, Y.223, E.227 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:V.164, E:M.216, E:T.219, E:Y.223, E:E.227 RB.11: 4 residues within 4Å: Chain F: R.407, D.413, D.441, T.443 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.413, F:D.441, F:T.443, H2O.26, H2O.27 RB.12: 6 residues within 4Å: Chain F: V.164, M.216, A.217, T.219, Y.223, E.227 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:V.164, F:M.216, F:T.219, F:Y.223, F:E.227

6 x ZN: ZINC ION(Non-covalent)

ZN.13: 4 residues within 4Å: Chain G: C.3, C.6, C.28, C.31 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.3, G:C.6, G:C.28, G:C.31 ZN.14: 4 residues within 4Å: Chain H: C.3, C.6, C.28, C.31 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.3, H:C.6, H:C.28, H:C.31 ZN.15: 4 residues within 4Å: Chain I: C.3, C.6, C.28, C.31 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.3, I:C.6, I:C.28, I:C.31 ZN.16: 4 residues within 4Å: Chain J: C.3, C.6, C.28, C.31 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.3, J:C.6, J:C.28, J:C.31 ZN.17: 4 residues within 4Å: Chain K: C.3, C.6, C.28, C.31 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.3, K:C.6, K:C.28, K:C.31 ZN.18: 4 residues within 4Å: Chain L: C.3, C.6, C.28, C.31 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.3, L:C.6, L:C.28, L:C.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marshall, S.A. et al., Domain mobility and allosteric activation of UbiD decarboxylases. To Be Published

Release Date

2021-08-25

Peptides

Phenolic acid decarboxylase: ABCDEF
Protein ShdD: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

F
A

G
b

H
c

I
d

J
e

K
f

L
a

Phenolic acid decarboxylase

Protein ShdD

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