SMTL ID : 6s0f.1

Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with 3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: W.279, V.308, N.346, T.352 Ligands: KDN.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.279 GOL.4: 10 residues within 4Å: Chain A: P.251, A.254, L.255, M.259, D.260, A.261, V.262, W.291 Chain B: I.290, Q.293 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.293, A:D.260, A:A.261, A:V.262 GOL.5: 8 residues within 4Å: Chain A: P.287, E.289, R.337, R.411, Y.480 Chain B: A.252, L.255, G.256 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.337, A:R.411, A:R.411, B:G.256 Water bridges: A:M.286, A:E.289, A:E.289, A:R.337, B:E.392 GOL.7: 5 residues within 4Å: Chain A: H.134, F.203, F.278, W.279 Ligands: KDN.10 No protein-ligand interaction detected (PLIP) GOL.8: 6 residues within 4Å: Chain A: E.212, G.256, A.389, P.390 Chain B: R.411, Y.480 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.411 GOL.9: 3 residues within 4Å: Chain A: K.45, T.301, R.341 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.45, A:K.45, A:T.301, A:R.341, A:R.341 GOL.11: 4 residues within 4Å: Chain A: A.162, E.163 Chain B: E.406, W.407 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.407 GOL.13: 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:M.259, B:D.260, B:A.261, B:V.262, A:Q.293 GOL.17: 3 residues within 4Å: Chain B: Y.313, D.315, P.399 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.315 GOL.18: 8 residues within 4Å: Chain A: A.252, L.255, G.256 Chain B: P.287, E.289, R.337, R.411, Y.480 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.337, B:R.411, B:R.411, A:A.252 Water bridges: B:Y.480

3 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.2: 3 residues within 4Å: Chain A: A.224, E.225, R.228 No protein-ligand interaction detected (PLIP) SCN.6: 3 residues within 4Å: Chain A: R.292, R.337, G.338 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.292 SCN.14: 4 residues within 4Å: Chain B: E.30, D.33, D.37, R.116 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 5 residues within 4Å: Chain A: R.177, I.218, A.221, F.222, E.225 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.177, A:I.218, A:A.221, A:F.222

2 x KDN: deamino-beta-neuraminic acid(Non-covalent)

KDN.10: 13 residues within 4Å: Chain A: D.14, N.15, S.16, C.53, W.95, R.129, H.134, R.202, W.279, N.346, T.352 Ligands: GOL.1, GOL.7 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.14, A:N.15, A:S.16, A:S.16, A:R.129, A:R.129, A:N.346, A:N.346, A:T.352, A:T.352 Water bridges: A:H.134 Salt bridges: A:R.129, A:H.134, A:R.202 KDN.19: 12 residues within 4Å: Chain B: D.14, N.15, S.16, C.53, W.95, R.129, H.134, R.202, W.279, F.345, N.346, T.352 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:D.14, B:D.14, B:N.15, B:S.16, B:R.129, B:R.129, B:N.346, B:N.346, B:N.346, B:T.352 Water bridges: B:H.134, B:Q.351 Salt bridges: B:R.129, B:H.134, B:R.202

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

ACT.12: 1 residues within 4Å: Chain B: Q.351 No protein-ligand interaction detected (PLIP) ACT.15: 4 residues within 4Å: Chain B: A.59, Q.61, H.103, R.190 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.61 Hydrogen bonds: B:A.59 Water bridges: B:H.103 Salt bridges: B:H.103, B:R.190 ACT.16: 5 residues within 4Å: Chain B: W.125, H.242, D.271, M.272, T.301 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.271 Salt bridges: B:H.242, B:R.341

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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