SMTL ID : 6sme.1

THE CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM PROPIONIBACTERIUM ACNES

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-12-mer

Ligands

18 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: Y.27, N.78, A.80, H.104, I.105, S.106 Ligand excluded by PLIP SO4.2: 2 residues within 4Å: Chain A: R.60, W.64 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain B: R.60, W.64 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain C: Y.27, N.78, H.104, I.105, S.106 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain C: R.38, L.133, K.134 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain C: R.60, W.64 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain E: Y.27, N.78, A.80, H.104, I.105, S.106 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain E: R.60, W.64 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain F: R.60, W.64 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain G: Y.27, N.78, H.104, I.105, S.106 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain G: R.38, L.133, K.134 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain G: R.60, W.64 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain I: Y.27, N.78, A.80, H.104, I.105, S.106 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain I: R.60, W.64 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain J: R.60, W.64 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain K: Y.27, N.78, H.104, I.105, S.106 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain K: R.38, L.133, K.134 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain K: R.60, W.64 Ligand excluded by PLIP

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: N.15, L.16, R.18, L.19, R.21, R.22, Y.27 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.18, A:R.21, A:R.22, A:R.22 Water bridges: A:G.20, A:Y.27 GOL.5: 9 residues within 4Å: Chain B: L.16, R.22, Y.27, N.78, A.80, H.104, I.105, S.106, I.108 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.22, B:N.78, B:H.104, B:I.105, B:S.106 Water bridges: B:H.84 GOL.9: 4 residues within 4Å: Chain C: H.116, H.117 Chain F: H.116, H.117 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:H.117, F:H.117 Water bridges: C:H.116, C:S.118, F:H.116, F:H.117 GOL.12: 7 residues within 4Å: Chain E: N.15, L.16, R.18, L.19, R.21, R.22, Y.27 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:R.18, E:R.21, E:R.22, E:R.22 Water bridges: E:G.20, E:Y.27 GOL.14: 9 residues within 4Å: Chain F: L.16, R.22, Y.27, N.78, A.80, H.104, I.105, S.106, I.108 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.22, F:N.78, F:H.104, F:I.105, F:S.106 Water bridges: F:H.84 GOL.18: 4 residues within 4Å: Chain G: H.116, H.117 Chain J: H.116, H.117 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain J Hydrogen bonds: G:H.117, J:H.117 Water bridges: G:H.116, G:S.118, J:H.116, J:H.117 GOL.21: 7 residues within 4Å: Chain I: N.15, L.16, R.18, L.19, R.21, R.22, Y.27 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:R.18, I:R.21, I:R.22, I:R.22 Water bridges: I:G.20, I:Y.27 GOL.23: 9 residues within 4Å: Chain J: L.16, R.22, Y.27, N.78, A.80, H.104, I.105, S.106, I.108 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:R.22, J:N.78, J:H.104, J:I.105, J:S.106 Water bridges: J:H.84 GOL.27: 4 residues within 4Å: Chain B: H.116, H.117 Chain K: H.116, H.117 6 PLIP interactions: 3 interactions with chain K, 3 interactions with chain B Hydrogen bonds: K:H.117, B:H.117 Water bridges: K:H.116, K:S.118, B:H.116, B:H.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodier, M. et al., Biomacromolecular charge chirality detected using chiral plasmonic nanostructures. Nanoscale Horiz. (2020)

Release Date

2020-07-08

Peptides

3-dehydroquinate dehydratase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

3-dehydroquinate dehydratase