SMTL ID : 6sxs.1

GH54 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: Y.155, D.157, N.185, S.186, T.187, G.411, T.412, K.413 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.413

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 7 residues within 4Å: Chain A: N.66, A.425, A.426, L.427, N.428, G.429 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.425, A:G.429 Water bridges: A:N.66

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

SO4.3: 5 residues within 4Å: Chain A: T.352, L.406, N.407, A.408 Ligands: PEG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.408 SO4.5: 2 residues within 4Å: Chain A: N.66 Ligands: NAG.2 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 5 residues within 4Å: Chain A: A.31, Q.34, T.45, Y.75, H.83 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.31 PGE.14: 4 residues within 4Å: Chain A: E.369, V.390, D.391, P.393 No protein-ligand interaction detected (PLIP)

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: Y.25, S.27, F.28, Q.77, S.78 No protein-ligand interaction detected (PLIP) EDO.13: 6 residues within 4Å: Chain A: E.331, V.332, V.333, I.476, E.477, T.478 No protein-ligand interaction detected (PLIP) EDO.15: 8 residues within 4Å: Chain A: R.345, N.355, T.356, Q.357, E.448, N.449, V.450 Ligands: ACT.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.356

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 7 residues within 4Å: Chain A: Y.342, T.356, H.446, Y.447, E.448, N.449, D.471 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.446, A:E.448, A:E.448, A:E.448, A:N.449, A:N.449 PEG.10: 5 residues within 4Å: Chain A: H.399, Y.400, N.401, F.402, Y.439 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.399, A:H.399, A:N.401, A:F.402 PEG.11: 7 residues within 4Å: Chain A: T.377, G.378, L.379, A.380, N.381, S.382 Ligands: ACT.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.382, A:S.382 PEG.12: 5 residues within 4Å: Chain A: R.398, Y.400, L.405, N.407 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.398, A:A.408

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

ACT.8: 7 residues within 4Å: Chain A: R.225, V.318, L.321, N.381, S.382, Q.383 Ligands: PEG.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.318, A:Q.383 Hydrogen bonds: A:N.381, A:Q.383 Salt bridges: A:R.225 ACT.16: 2 residues within 4Å: Chain A: R.345 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.345, A:R.345 Salt bridges: A:R.345

1 x LX5: [(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl] hydrogen sulfate(Covalent)

LX5.9: 16 residues within 4Å: Chain A: C.159, C.160, D.162, D.172, M.178, W.189, D.202, M.203, E.204, N.205, N.206, L.207, G.278, G.279, D.280, S.282 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.204 Hydrogen bonds: A:D.162, A:D.172, A:W.189, A:E.204, A:N.205, A:N.205, A:N.206, A:N.206, A:G.279, A:D.280, A:D.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGregor, N.G.S. et al., Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining alpha-l-Arabinofuranosidases. J.Am.Chem.Soc. (2020)

Release Date

2020-02-26

Peptides

Alpha-L-arabinofuranosidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Alpha-L-arabinofuranosidase B

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