SMTL ID : 6rzd.1

Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: D.14, R.129, H.134, R.202, W.279, F.345, N.346 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.346 Water bridges: A:H.134 Salt bridges: A:R.129, A:H.134, A:R.202 SO4.12: 8 residues within 4Å: Chain B: D.14, R.129, H.134, R.202, F.345, N.346 Ligands: TAM.11, GOL.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.14, B:N.346, B:N.346 Salt bridges: B:R.129, B:H.134, B:R.202

2 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.2: 7 residues within 4Å: Chain A: W.279, V.308, L.309, F.319, T.321, Q.351, T.352 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.279, A:T.352 TAM.11: 10 residues within 4Å: Chain B: W.279, V.308, L.309, F.319, T.321, N.346, Q.351, T.352, A.353 Ligands: SO4.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.308, B:T.352 Hydrogen bonds: B:N.346, B:A.353 Water bridges: B:N.346, B:T.352

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

ACT.3: 3 residues within 4Å: Chain A: G.172, R.173, A.174 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.174 Hydrogen bonds: A:A.174 Salt bridges: A:R.173 ACT.6: 3 residues within 4Å: Chain A: R.266, E.296, T.298 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.266 ACT.8: 1 residues within 4Å: Chain A: R.140 No protein-ligand interaction detected (PLIP) ACT.9: 3 residues within 4Å: Chain A: P.79, L.80, R.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.79, A:R.149 ACT.10: 3 residues within 4Å: Chain A: Q.104, D.105, G.106 No protein-ligand interaction detected (PLIP) ACT.14: 6 residues within 4Å: Chain A: W.388, P.393, A.395 Chain B: W.388, A.395 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.388 ACT.18: 1 residues within 4Å: Chain B: K.45 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.45 ACT.19: 2 residues within 4Å: Chain B: D.37, R.120 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.120

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: D.14, N.15, S.16, C.53, W.95, R.129, H.134 Ligands: SO4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.14, A:N.15, A:H.134 Water bridges: A:H.134 GOL.5: 5 residues within 4Å: Chain A: R.250, D.285, P.287 Chain B: P.393 Ligands: ACT.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.285 Water bridges: A:D.285 GOL.7: 8 residues within 4Å: Chain A: R.411, Y.480, N.481, L.482 Chain B: G.210, E.212, G.256, P.390 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.212, B:G.256, A:R.411, A:N.481 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: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.260, B:A.261, B:V.262, A:Q.293, A:Q.293 GOL.15: 7 residues within 4Å: Chain B: D.14, N.15, S.16, C.53, W.95, H.134 Ligands: SO4.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.14, B:N.15, B:S.16 Water bridges: B:D.132, B:Y.135 GOL.16: 9 residues within 4Å: Chain A: G.210, E.212, G.256, A.389, P.390 Chain B: R.411, Y.480, N.481, L.482 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.411, B:N.481, A:P.390 Water bridges: B:Y.480 GOL.17: 9 residues within 4Å: Chain B: P.437, E.438, L.440, E.441, V.442, L.448, C.449, A.450, F.451 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.437, B:V.442, B:V.442, B:F.451

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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