SMTL ID : 6s04.1

Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with N-glycolylneuraminic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: W.279, N.346, T.352 Ligands: NGE.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.279 Hydrogen bonds: A:N.346 ACT.2: 4 residues within 4Å: Chain A: G.172, R.173, A.174, E.175 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.174 Hydrogen bonds: A:A.174, A:E.175 Salt bridges: A:R.173 ACT.7: 4 residues within 4Å: Chain A: W.388, A.395 Chain B: W.388, A.395 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.388, A:A.395 Hydrogen bonds: A:P.393 Water bridges: B:R.250 ACT.9: 3 residues within 4Å: Chain B: R.155, F.161, R.167 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.167 Salt bridges: B:R.167

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: Q.104, D.105, G.106 No protein-ligand interaction detected (PLIP) GOL.5: 4 residues within 4Å: Chain A: E.406, W.407 Chain B: A.162, E.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.407 GOL.6: 10 residues within 4Å: Chain A: I.290, Q.293 Chain B: P.251, A.254, L.255, M.259, D.260, A.261, V.262, W.291 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.260, B:D.260, B:A.261, B:V.262, A:Q.293 GOL.8: 4 residues within 4Å: Chain B: R.443, E.447, L.448, P.472 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.443, B:E.447, B:L.448

2 x NGE: N-glycolyl-beta-neuraminic acid(Non-covalent)

NGE.4: 16 residues within 4Å: Chain A: D.14, N.15, S.16, Y.20, C.53, W.95, R.129, H.134, Y.135, R.202, W.279, F.345, N.346, Q.351, T.352 Ligands: ACT.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.15, A:N.15, A:S.16, A:S.16, A:S.16, A:R.129, A:R.129, A:Y.135, A:N.346, A:Q.351, A:T.352 Water bridges: A:H.134, A:Y.135, A:Y.135, A:Q.351 Salt bridges: A:R.129, A:H.134, A:R.202 NGE.10: 14 residues within 4Å: Chain B: D.14, N.15, S.16, Y.20, C.53, W.95, R.129, H.134, R.202, W.279, F.345, N.346, Q.351, T.352 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:D.14, B:N.15, B:N.15, B:S.16, B:S.16, B:S.16, B:R.129, B:R.129, B:Y.135, B:Y.135, B:N.346, B:N.346, B:Q.351 Water bridges: B:H.134, B:Q.351, B:Q.351 Salt bridges: B:R.129, B:H.134, B:R.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bule, P. et al., Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action. Nat Commun (2019)

Release Date

2019-11-06

Peptides

exosialidase from uncultured bacterium pG7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

exosialidase from uncultured bacterium pG7

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