SMTL ID : 7xr9.1

Crystal structure of DgpA with glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-hexamer

Ligands

5 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.1: 9 residues within 4Å: Chain A: K.101, R.160, P.165, W.167, F.170, D.183, I.184, H.187 Ligands: NAD.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.101, A:R.160, A:R.160, A:D.183, A:H.187 Salt bridges: A:R.160 BGC.4: 7 residues within 4Å: Chain C: R.160, P.165, F.170, D.183, H.187, E.265 Ligands: NAD.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.160, C:D.183, C:H.187 Salt bridges: C:R.160 BGC.6: 8 residues within 4Å: Chain D: K.101, R.160, P.165, W.167, F.170, D.183, H.187 Ligands: NAD.7 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.160, D:R.160, D:D.183, D:H.187, D:H.187, D:W.256 Salt bridges: D:R.160 BGC.8: 8 residues within 4Å: Chain E: K.101, R.160, P.165, F.170, D.183, I.184, H.187 Ligands: NAD.9 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:K.101, E:R.160, E:R.160, E:D.183, E:H.187, E:H.187 Salt bridges: E:R.160 BGC.10: 8 residues within 4Å: Chain F: K.101, R.160, P.165, W.167, D.183, I.184, H.187 Ligands: NAD.11 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:K.101, F:K.101, F:R.160, F:R.160, F:H.187, F:H.187 Salt bridges: F:R.160

6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 22 residues within 4Å: Chain A: I.10, G.11, G.13, G.14, I.15, D.61, Y.62, C.77, T.78, P.79, N.80, H.83, E.100, K.101, P.102, G.127, Q.129, V.169, F.170, Q.176, H.187 Ligands: BGC.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.15, A:I.15, A:F.170 Hydrogen bonds: A:G.14, A:I.15, A:T.78, A:N.80, A:S.82, A:Q.129, A:Q.129, A:Q.176 NAD.3: 25 residues within 4Å: Chain B: I.10, G.11, C.12, G.13, G.14, I.15, D.38, I.39, Q.40, R.43, C.77, T.78, P.79, N.80, H.83, E.100, K.101, P.102, G.127, Q.129, W.167, G.168, F.170, D.183, H.187 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.15, B:K.101 Hydrogen bonds: B:G.13, B:G.14, B:I.15, B:I.39, B:Q.40, B:R.43, B:T.78, B:N.80, B:K.101, B:Q.129, B:Q.129 pi-Cation interactions: B:K.101 NAD.5: 25 residues within 4Å: Chain C: I.10, G.11, G.13, G.14, I.15, C.37, D.38, I.39, R.43, Y.62, C.77, T.78, P.79, N.80, H.83, E.100, K.101, P.102, G.127, Q.129, V.169, F.170, Q.176, H.187 Ligands: BGC.4 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.15, C:F.170 Hydrogen bonds: C:G.14, C:I.15, C:I.39, C:R.43, C:N.80, C:N.80, C:H.83, C:K.101, C:Q.129, C:Q.129, C:Q.176 pi-Cation interactions: C:K.101 NAD.7: 23 residues within 4Å: Chain D: I.10, G.11, C.12, G.13, G.14, I.15, D.38, I.39, Q.40, C.77, T.78, P.79, N.80, H.83, E.100, K.101, P.102, G.127, Q.129, W.167, F.170, H.187 Ligands: BGC.6 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.15 Hydrogen bonds: D:C.12, D:G.13, D:I.15, D:I.39, D:T.78, D:N.80, D:N.80, D:K.101, D:Q.129, D:Q.129 pi-Cation interactions: D:K.101 NAD.9: 24 residues within 4Å: Chain E: G.11, G.13, G.14, I.15, C.37, D.38, I.39, R.43, Y.62, C.77, T.78, P.79, N.80, H.83, E.100, K.101, P.102, G.127, Q.129, V.169, F.170, Q.176, H.187 Ligands: BGC.8 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:I.15, E:F.170 Hydrogen bonds: E:G.14, E:I.15, E:I.39, E:T.78, E:N.80, E:N.80, E:Q.129, E:Q.129, E:Q.176 Water bridges: E:G.13, E:A.16, E:S.82 pi-Cation interactions: E:K.101 NAD.11: 24 residues within 4Å: Chain F: G.11, G.13, G.14, I.15, K.19, C.37, D.38, I.39, R.43, C.77, T.78, P.79, N.80, H.83, E.100, K.101, P.102, G.127, Q.129, W.167, G.168, F.170, H.187 Ligands: BGC.10 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:I.15 Hydrogen bonds: F:G.14, F:I.15, F:K.19, F:I.39, F:T.78, F:N.80, F:K.101, F:Q.129, F:Q.129, F:D.183, F:D.183 pi-Cation interactions: F:K.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, P. et al., Structural mechanism of a dual-functional enzyme DgpA/B/C as both a C -glycoside cleaving enzyme and an O - to C -glycoside isomerase. Acta Pharm Sin B (2023)

Release Date

2023-04-05

Peptides

DgpA: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

DgpA

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