SMTL ID : 7ae4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.31 Å

Oligo State

hetero-6-6-mer

Ligands

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 5 residues within 4Å: Chain A: F.391, Q.399, W.402 Chain E: I.312, P.313 No protein-ligand interaction detected (PLIP) PEG.15: 7 residues within 4Å: Chain B: I.312, P.313, W.314 Chain C: F.391, E.398, Q.399, W.402 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.399 PEG.21: 7 residues within 4Å: Chain D: F.391, Q.399, W.402, L.457 Chain F: I.312, P.313, W.314 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.399 PEG.28: 5 residues within 4Å: Chain A: E.398 Chain E: G.45, W.71, W.314, Y.319 No protein-ligand interaction detected (PLIP) PEG.30: 7 residues within 4Å: Chain A: I.312, P.313, W.314 Chain E: F.391, Q.399, W.402, L.457 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.399 PEG.36: 7 residues within 4Å: Chain D: I.312, P.313, W.314 Chain F: F.391, E.398, Q.399, W.402 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.399

15 x NA: SODIUM ION(Non-functional Binders)

NA.2: 7 residues within 4Å: Chain A: V.164, M.216, A.217, T.219, E.227 Ligands: PO4.5, MG.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.216, A:T.219 NA.3: 5 residues within 4Å: Chain A: R.407, K.412, D.413, D.441, T.443 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.412, A:T.443 NA.4: 8 residues within 4Å: Chain A: N.160, L.162, N.163, G.222, Y.223, N.224, Q.225, N.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.160, A:N.163, A:Q.225 NA.9: 7 residues within 4Å: Chain B: V.164, M.216, A.217, T.219, E.227 Ligands: PO4.12, MG.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.219, B:E.227 NA.10: 5 residues within 4Å: Chain B: R.407, K.412, D.413, D.441, T.443 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.412, B:D.441, B:T.443 NA.11: 6 residues within 4Å: Chain B: N.160, L.162, N.163, Y.223, Q.225, N.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.223, B:Q.225 NA.16: 7 residues within 4Å: Chain C: V.164, M.216, A.217, T.219, E.227 Ligands: PO4.18, MG.19 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.164, C:T.219 NA.17: 5 residues within 4Å: Chain C: R.407, K.412, D.413, D.441, T.443 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.413, C:T.443 NA.22: 7 residues within 4Å: Chain D: V.164, M.216, A.217, T.219, E.227 Ligands: PO4.24, MG.25 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.217, D:T.219 NA.23: 5 residues within 4Å: Chain D: R.407, K.412, D.413, D.441, T.443 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.412, D:K.412, D:T.443 NA.31: 5 residues within 4Å: Chain E: R.407, K.412, D.413, D.441, T.443 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.413, E:T.443 NA.32: 7 residues within 4Å: Chain E: V.164, M.216, A.217, T.219, E.227 Ligands: PO4.34, MG.35 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.219, E:T.219 NA.33: 7 residues within 4Å: Chain E: N.160, L.162, N.163, Y.223, Q.225, N.226, E.227 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.225, E:E.227 NA.37: 7 residues within 4Å: Chain F: V.164, M.216, A.217, T.219, E.227 Ligands: PO4.39, MG.40 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.219, F:T.219 NA.38: 5 residues within 4Å: Chain F: R.407, K.412, D.413, D.441, T.443 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.441, F:T.443

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 8 residues within 4Å: Chain A: Y.167, H.185, D.186, A.217, T.219, E.227 Ligands: NA.2, MG.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.167, A:D.186, A:D.186, A:A.217 Salt bridges: A:H.185 PO4.12: 11 residues within 4Å: Chain B: N.163, V.164, G.165, Y.167, H.185, D.186, A.217, T.219, E.227 Ligands: NA.9, MG.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.167, B:Y.167, B:D.186 Salt bridges: B:H.185 PO4.18: 9 residues within 4Å: Chain C: G.165, Y.167, H.185, D.186, A.217, T.219, E.227 Ligands: NA.16, MG.19 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.167, C:Y.167, C:Y.167, C:D.186, C:D.186, C:D.186 Salt bridges: C:H.185 PO4.24: 10 residues within 4Å: Chain D: V.164, G.165, Y.167, H.185, D.186, A.217, T.219, E.227 Ligands: NA.22, MG.25 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.167, D:Y.167, D:D.186 Salt bridges: D:H.185 PO4.34: 10 residues within 4Å: Chain E: N.163, G.165, Y.167, H.185, D.186, A.217, T.219, E.227 Ligands: NA.32, MG.35 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.167, E:Y.167, E:D.186, E:D.186 Salt bridges: E:H.185 PO4.39: 8 residues within 4Å: Chain F: Y.167, H.185, D.186, A.217, T.219, E.227 Ligands: NA.37, MG.40 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Y.167, F:Y.167, F:D.186

6 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 7 residues within 4Å: Chain A: N.163, D.186, V.221, G.222, E.227 Ligands: NA.2, PO4.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.186, A:E.227 MG.13: 6 residues within 4Å: Chain B: N.163, D.186, V.221, E.227 Ligands: NA.9, PO4.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.186, B:E.227 MG.19: 6 residues within 4Å: Chain C: N.163, D.186, V.221, E.227 Ligands: NA.16, PO4.18 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.186, C:E.227 MG.25: 5 residues within 4Å: Chain D: N.163, D.186, E.227 Ligands: NA.22, PO4.24 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.186, D:E.227 MG.35: 6 residues within 4Å: Chain E: N.163, D.186, V.221, E.227 Ligands: NA.32, PO4.34 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.186, E:E.227 MG.40: 7 residues within 4Å: Chain F: N.163, D.186, V.221, G.222, E.227 Ligands: NA.37, PO4.39 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.186, F:E.227

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

CL.7: 3 residues within 4Å: Chain A: G.285, R.287 Chain E: R.453 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.453, E.454 Chain E: R.287 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: R.287 Chain C: R.453 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: R.453, E.454 Chain C: R.287 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain D: G.285, R.287 Chain F: R.453, E.454 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain D: R.453 Chain F: G.285, R.287 Ligand excluded by PLIP

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.29: 6 residues within 4Å: Chain E: T.166, E.278, L.310, I.317, M.321, H.349 No protein-ligand interaction detected (PLIP)

6 x ZN: ZINC ION(Non-covalent)

ZN.41: 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.42: 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.43: 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.44: 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.45: 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.46: 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
A

B
B

C
C

D
D

E
E

F
F

G
a

H
b

I
c

J
d

K
e

L
f

Phenolic acid decarboxylase

Protein ShdD

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