SMTL ID : 7xre.1

Crystal structure of DgpA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

homo-hexamer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: I.10, G.11, C.12, G.13, G.14, I.15, K.19, C.37, I.39, Q.40, 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, H.187 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.15, A:F.170 Hydrogen bonds: A:C.12, A:G.14, A:I.15, A:Q.40, A:Q.40, A:R.43, A:N.80, A:H.83, A:E.100, A:Q.129, A:Q.129 pi-Cation interactions: A:K.101 NAD.2: 23 residues within 4Å: Chain B: G.11, 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, Q.129, W.167, F.170, H.187 Chain C: A.312, Y.313, F.314 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.15, B:I.15, C:F.314 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:E.100, B:Q.129 pi-Cation interactions: B:K.101 NAD.3: 23 residues within 4Å: Chain C: G.11, C.12, G.13, G.14, I.15, D.38, I.39, Q.40, C.77, T.78, P.79, N.80, S.82, H.83, E.100, K.101, P.102, G.127, Q.129, V.169, F.170, Q.176, H.187 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.170 Hydrogen bonds: C:C.12, C:G.14, C:I.15, C:I.39, C:N.80, C:N.80, C:S.82, C:E.100, C:K.101, C:Q.129, C:Q.129, C:Q.176 pi-Cation interactions: C:K.101 NAD.4: 24 residues within 4Å: Chain D: I.10, 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 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.15 Hydrogen bonds: D:G.13, D:G.13, D:I.15, D:K.19, D:I.39, D:P.79, D:N.80, D:Q.129, D:Q.129 NAD.5: 23 residues within 4Å: Chain E: G.11, G.13, G.14, I.15, K.19, D.38, I.39, R.43, C.77, T.78, P.79, N.80, S.82, H.83, E.100, K.101, P.102, G.127, Q.129, V.169, F.170, Q.176, H.187 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:I.15, E:K.101, E:F.170 Hydrogen bonds: E:G.14, E:I.15, E:I.39, E:Q.40, E:R.43, E:N.80, E:S.82, E:Q.129, E:Q.129, E:Q.176, E:Q.176 pi-Cation interactions: E:K.101 NAD.6: 23 residues within 4Å: Chain F: G.11, C.12, G.13, G.14, I.15, D.38, 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, Q.176, H.187 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:I.15 Hydrogen bonds: F:C.12, F:G.14, F:I.15, F:R.43, F:T.78, F:Q.129, F:Q.129, F:Q.176 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

2023-02-15

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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