SMTL ID : 7exz.1 (1 other biounit)

DgpB-DgpC complex apo 2.5 angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-4-3-mer

Ligands

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

MN.1: 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.8: 4 residues within 4Å: Chain C: E.141, D.173, H.263, E.299 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.141, C:H.263, C:E.299, H2O.6, H2O.6 MN.12: 5 residues within 4Å: Chain D: E.141, H.143, D.173, H.263, E.299 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.141, D:D.173, D:H.263, D:E.299, H2O.8, H2O.8 MN.18: 4 residues within 4Å: Chain F: E.141, D.173, H.263, E.299 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.141, F:H.263, F:E.299, H2O.13, H2O.14

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: Y.11, V.42, N.78, R.114, Q.116 Chain B: Y.39 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.78, A:N.78, A:R.114, A:R.114, B:Y.39 Water bridges: A:E.299, A:E.299, A:E.301 GOL.9: 5 residues within 4Å: Chain C: V.42, N.78, R.114, Q.116, E.299 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.78, C:N.78, C:R.114, C:R.114, C:Q.116 Water bridges: C:E.299, C:E.301 GOL.13: 6 residues within 4Å: Chain D: Y.11, V.42, N.78, R.114, Q.116 Chain E: Y.39 12 PLIP interactions: 11 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 Water bridges: D:Y.11, D:Y.11, D:E.40, D:E.299, D:E.299, D:E.301, E:Y.39 GOL.19: 7 residues within 4Å: Chain F: Y.11, V.42, N.78, R.114, Q.116, E.299 Chain G: Y.39 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.78, F:N.78, F:R.114, F:Q.116

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

SO4.3: 4 residues within 4Å: Chain A: G.85, D.86, R.87 Chain B: T.125 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.125 Water bridges: A:R.87 SO4.6: 5 residues within 4Å: Chain B: F.21, W.22, K.95 Chain C: Y.67 Chain D: Y.134 6 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:W.22, D:Y.134, D:Y.134 Water bridges: B:W.22, C:Y.68 Salt bridges: B:K.95 SO4.7: 8 residues within 4Å: Chain B: E.62, N.63, I.64, S.65, G.74 Chain D: V.99, K.103, F.130 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.62, B:S.65 Water bridges: B:I.64, B:I.64, B:G.74 Salt bridges: D:K.103 SO4.10: 7 residues within 4Å: Chain C: A.178, K.180, N.182, L.239, T.240, H.267, A.277 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.182, C:T.240 Salt bridges: C:H.267 SO4.11: 6 residues within 4Å: Chain C: C.65, Q.66, D.69, M.70, E.71, P.72 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.70 SO4.14: 8 residues within 4Å: Chain D: A.178, K.180, N.182, L.239, T.240, H.267, A.277, I.278 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.182 Salt bridges: D:H.267 SO4.16: 4 residues within 4Å: Chain E: I.47, D.48, E.49, L.78 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:D.48 Water bridges: E:I.47, E:I.50, E:H.79, E:H.79 SO4.17: 6 residues within 4Å: Chain E: K.19, N.20, Q.31, N.142 Chain F: E.25, Y.68 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:Y.68, E:N.20, E:N.142 Water bridges: F:R.29 Salt bridges: E:K.19 SO4.20: 3 residues within 4Å: Chain F: V.99, K.103, F.130 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:K.103 SO4.21: 4 residues within 4Å: Chain F: V.53, S.54, D.55, K.107 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.53, F:D.55 Salt bridges: F:K.107 SO4.22: 7 residues within 4Å: Chain F: A.178, K.180, P.181, N.182, L.239, H.267, A.277 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.182 Salt bridges: F:H.267 SO4.23: 1 residues within 4Å: Chain F: K.196 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:K.196 SO4.25: 8 residues within 4Å: Chain C: Y.134 Chain D: Y.67 Chain G: F.21, W.22, A.23, I.28, E.72, K.95 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:W.22 Water bridges: G:W.22 Salt bridges: G:K.95 SO4.26: 5 residues within 4Å: Chain D: E.25, Y.68 Chain G: K.19, N.20, Q.31 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:Y.68, G:Q.31 Salt bridges: G:K.19

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

EPE.4: 8 residues within 4Å: Chain B: I.47, D.48, E.49, I.50, A.61, V.75, L.78, H.79 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.50 Water bridges: B:H.79, B:H.79 EPE.5: 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, B:S.135 Salt bridges: B:D.11 EPE.15: 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 EPE.24: 7 residues within 4Å: Chain G: R.6, D.11, V.12, V.13, G.134, S.135, K.136 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:R.6, G:V.12, G:V.13, G:S.135 Salt bridges: G:D.11, G: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

2021-11-03

Peptides

AP_endonuc_2 domain-containing protein: ACDF
DgpB: BEG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
E

F
G

B
B

E
F

G
H

AP_endonuc_2 domain-containing protein

DgpB

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