SMTL ID : 7bvr.2 (1 other biounit)

DgpB-DgpC complex apo

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-3-3-mer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: V.42, N.78, R.114, Q.116, E.299 Chain B: Y.39 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.78, A:N.78, A:R.114, A:R.114, A:Q.116, A:E.299 GOL.6: 8 residues within 4Å: Chain D: V.42, N.78, R.114, Q.116, E.141, E.299 Chain E: Y.39 Ligands: MN.7 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:N.78, D:N.78, D:R.114, D:R.114, D:Q.116, D:E.141, E:Y.39 Water bridges: D:E.299 GOL.9: 6 residues within 4Å: Chain F: Y.11, V.42, N.78, R.114, Q.116, E.299 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:N.78, F:N.78, F:R.114, F:R.114, F:Q.116

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: E.141, H.143, D.173, H.263, E.299 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.141, A:D.173, A:H.263, A:E.299, H2O.1 MN.7: 6 residues within 4Å: Chain D: E.141, H.143, D.173, H.263, E.299 Ligands: GOL.6 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.141, D:D.173, D:H.263, D:E.299, H2O.6 MN.10: 5 residues within 4Å: Chain F: E.141, H.143, D.173, H.263, E.299 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.141, F:D.173, F:H.263, F:E.299, H2O.11

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 7 residues within 4Å: Chain B: I.47, D.48, E.49, I.50, A.61, V.75, L.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.50 Water bridges: B:H.79 EPE.4: 7 residues within 4Å: Chain B: R.6, D.11, V.12, V.13, G.134, S.135, K.136 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.6, B:V.12, B:V.13, B:S.135 Salt bridges: B:D.11, B:K.136 EPE.5: 7 residues within 4Å: Chain C: R.6, D.11, V.12, V.13, G.134, S.135, K.136 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.6, C:V.12, C:V.13, C:V.13, C:S.135 Salt bridges: C:D.11, C:K.136 EPE.8: 7 residues within 4Å: Chain E: R.6, D.11, V.12, V.13, G.134, S.135, K.136 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:R.6, E:V.12, E:V.13, E:S.135 Salt bridges: E:D.11, E:K.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mori, T. et al., C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes. Nat Commun (2021)

Release Date

2021-04-14

Peptides

AP_endonuc_2 domain-containing protein: ADF
DgpB: BCE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

F
G

B
B

C
D

E
F

AP_endonuc_2 domain-containing protein

DgpB

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