SMTL ID : 6smf.1

THE CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM ZYMOMONAS MOBILIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-12-mer

Ligands

12 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 11 residues within 4Å: Chain A: L.18, N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.83 Hydrogen bonds: A:N.81, A:A.83, A:H.107, A:L.108, A:S.109, A:S.109 Salt bridges: A:H.87, A:H.107, A:R.114, A:R.118 FLC.4: 10 residues within 4Å: Chain B: N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.81, B:N.81, B:H.107, B:L.108, B:S.109 Salt bridges: B:H.87, B:H.107, B:R.114, B:R.114, B:R.118 FLC.6: 10 residues within 4Å: Chain C: N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.81, C:A.83, C:H.107, C:L.108, C:S.109, C:S.109 Salt bridges: C:H.87, C:H.107, C:H.107, C:R.114, C:R.118 FLC.7: 11 residues within 4Å: Chain D: L.18, N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:A.83 Hydrogen bonds: D:N.81, D:N.81, D:A.83, D:H.107, D:L.108, D:S.109 Water bridges: D:R.114, D:R.114 Salt bridges: D:H.87, D:H.107, D:R.114, D:R.118 FLC.10: 11 residues within 4Å: Chain E: L.18, N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:A.83 Hydrogen bonds: E:N.81, E:A.83, E:H.107, E:L.108, E:S.109, E:S.109 Salt bridges: E:H.87, E:H.107, E:R.114, E:R.118 FLC.13: 10 residues within 4Å: Chain F: N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:N.81, F:N.81, F:H.107, F:L.108, F:S.109 Salt bridges: F:H.87, F:H.107, F:R.114, F:R.114, F:R.118 FLC.15: 10 residues within 4Å: Chain G: N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:N.81, G:A.83, G:H.107, G:L.108, G:S.109, G:S.109 Salt bridges: G:H.87, G:H.107, G:H.107, G:R.114, G:R.118 FLC.16: 11 residues within 4Å: Chain H: L.18, N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:A.83 Hydrogen bonds: H:N.81, H:N.81, H:A.83, H:H.107, H:L.108, H:S.109 Water bridges: H:R.114, H:R.114 Salt bridges: H:H.87, H:H.107, H:R.114, H:R.118 FLC.19: 11 residues within 4Å: Chain I: L.18, N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:A.83 Hydrogen bonds: I:N.81, I:A.83, I:H.107, I:L.108, I:S.109, I:S.109 Salt bridges: I:H.87, I:H.107, I:R.114, I:R.118 FLC.22: 10 residues within 4Å: Chain J: N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:N.81, J:N.81, J:H.107, J:L.108, J:S.109 Salt bridges: J:H.87, J:H.107, J:R.114, J:R.114, J:R.118 FLC.24: 10 residues within 4Å: Chain K: N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:N.81, K:A.83, K:H.107, K:L.108, K:S.109, K:S.109 Salt bridges: K:H.87, K:H.107, K:H.107, K:R.114, K:R.118 FLC.25: 11 residues within 4Å: Chain L: L.18, N.81, A.83, A.84, H.87, H.107, L.108, S.109, P.111, R.114, R.118 13 PLIP interactions: 13 interactions with chain L Hydrophobic interactions: L:A.83 Hydrogen bonds: L:N.81, L:N.81, L:A.83, L:H.107, L:L.108, L:S.109 Water bridges: L:R.114, L:R.114 Salt bridges: L:H.87, L:H.107, L:R.114, L:R.118

6 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 10 residues within 4Å: Chain A: E.60, T.88, S.89 Chain B: E.60, T.88, S.89 Chain C: E.60, Y.85, T.88, S.89 7 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:T.88, C:T.88, A:E.60, A:T.88, B:T.88 Water bridges: C:E.60, B:V.90 TRS.8: 11 residues within 4Å: Chain D: E.60, T.88, S.89 Chain H: E.60, T.88, S.89 Chain L: E.60, T.88, S.89 Ligands: TRS.17, TRS.26 8 PLIP interactions: 3 interactions with chain H, 2 interactions with chain L, 3 interactions with chain D Hydrogen bonds: H:E.60, H:T.88, L:E.60, L:T.88, D:E.60, D:T.88 Water bridges: H:V.90, D:V.90 TRS.11: 10 residues within 4Å: Chain E: E.60, T.88, S.89 Chain F: E.60, T.88, S.89 Chain G: E.60, Y.85, T.88, S.89 7 PLIP interactions: 3 interactions with chain G, 2 interactions with chain E, 2 interactions with chain F Hydrogen bonds: G:T.88, G:T.88, E:E.60, E:T.88, F:T.88 Water bridges: G:E.60, F:V.90 TRS.17: 11 residues within 4Å: Chain D: E.60, T.88, S.89 Chain H: E.60, T.88, S.89 Chain L: E.60, T.88, S.89 Ligands: TRS.8, TRS.26 8 PLIP interactions: 2 interactions with chain D, 3 interactions with chain H, 3 interactions with chain L Hydrogen bonds: D:E.60, D:T.88, H:E.60, H:T.88, L:E.60, L:T.88 Water bridges: H:V.90, L:V.90 TRS.20: 10 residues within 4Å: Chain I: E.60, T.88, S.89 Chain J: E.60, T.88, S.89 Chain K: E.60, Y.85, T.88, S.89 7 PLIP interactions: 2 interactions with chain J, 3 interactions with chain K, 2 interactions with chain I Hydrogen bonds: J:T.88, K:T.88, K:T.88, I:E.60, I:T.88 Water bridges: J:V.90, K:E.60 TRS.26: 11 residues within 4Å: Chain D: E.60, T.88, S.89 Chain H: E.60, T.88, S.89 Chain L: E.60, T.88, S.89 Ligands: TRS.8, TRS.17 8 PLIP interactions: 3 interactions with chain D, 2 interactions with chain H, 3 interactions with chain L Hydrogen bonds: D:E.60, D:T.88, H:E.60, H:T.88, L:E.60, L:T.88 Water bridges: D:V.90, L:V.90

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

SO4.3: 9 residues within 4Å: Chain A: H.59, E.60, G.61 Chain B: H.59, E.60, G.61 Chain C: H.59, E.60, G.61 13 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C, 4 interactions with chain A Hydrogen bonds: B:G.61, C:G.61, A:G.61 Water bridges: B:E.60, C:E.60, C:E.60, C:E.60, C:E.60, A:E.60, A:E.60 Salt bridges: B:H.59, C:H.59, A:H.59 SO4.9: 11 residues within 4Å: Chain D: H.59, E.60, G.61 Chain H: H.59, E.60, G.61 Chain L: H.59, E.60, G.61 Ligands: SO4.18, SO4.27 12 PLIP interactions: 4 interactions with chain H, 5 interactions with chain L, 3 interactions with chain D Hydrogen bonds: H:G.61, L:G.61, D:G.61 Water bridges: H:E.60, H:E.60, L:E.60, L:E.60, L:E.60, D:E.60 Salt bridges: H:H.59, L:H.59, D:H.59 SO4.12: 9 residues within 4Å: Chain E: H.59, E.60, G.61 Chain F: H.59, E.60, G.61 Chain G: H.59, E.60, G.61 13 PLIP interactions: 6 interactions with chain G, 3 interactions with chain F, 4 interactions with chain E Hydrogen bonds: G:G.61, F:G.61, E:G.61 Water bridges: G:E.60, G:E.60, G:E.60, G:E.60, F:E.60, E:E.60, E:E.60 Salt bridges: G:H.59, F:H.59, E:H.59 SO4.18: 11 residues within 4Å: Chain D: H.59, E.60, G.61 Chain H: H.59, E.60, G.61 Chain L: H.59, E.60, G.61 Ligands: SO4.9, SO4.27 12 PLIP interactions: 3 interactions with chain H, 4 interactions with chain L, 5 interactions with chain D Hydrogen bonds: H:G.61, L:G.61, D:G.61 Water bridges: H:E.60, L:E.60, L:E.60, D:E.60, D:E.60, D:E.60 Salt bridges: H:H.59, L:H.59, D:H.59 SO4.21: 9 residues within 4Å: Chain I: H.59, E.60, G.61 Chain J: H.59, E.60, G.61 Chain K: H.59, E.60, G.61 13 PLIP interactions: 3 interactions with chain J, 6 interactions with chain K, 4 interactions with chain I Hydrogen bonds: J:G.61, K:G.61, I:G.61 Water bridges: J:E.60, K:E.60, K:E.60, K:E.60, K:E.60, I:E.60, I:E.60 Salt bridges: J:H.59, K:H.59, I:H.59 SO4.27: 11 residues within 4Å: Chain D: H.59, E.60, G.61 Chain H: H.59, E.60, G.61 Chain L: H.59, E.60, G.61 Ligands: SO4.9, SO4.18 12 PLIP interactions: 5 interactions with chain H, 3 interactions with chain L, 4 interactions with chain D Hydrogen bonds: H:G.61, L:G.61, D:G.61 Water bridges: H:E.60, H:E.60, H:E.60, L:E.60, D:E.60, D:E.60 Salt bridges: H:H.59, L:H.59, D:H.59

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain B: H.119 Chain G: H.119, K.120 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain G Hydrogen bonds: B:H.119, G:H.119, G:K.120 Water bridges: B:H.112 GOL.14: 3 residues within 4Å: Chain F: H.119 Chain K: H.119, K.120 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain K Hydrogen bonds: F:H.119, K:H.119, K:K.120 Water bridges: F:H.112 GOL.23: 3 residues within 4Å: Chain C: H.119, K.120 Chain J: H.119 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain J Hydrogen bonds: C:H.119, C:K.120, J:H.119 Water bridges: J:H.112

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