SMTL ID : 6sxt.1

GH54 a-l-arabinofuranosidase soaked with aziridine inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 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: 9 residues within 4Å: Chain A: Y.156, D.158, N.186, S.187, T.188, T.413, K.414, Q.415 Ligands: EDO.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.414 Water bridges: A:Q.415

1 x ALA: ALANINE(Non-covalent)

ALA.2: 5 residues within 4Å: Chain A: V.333, V.391, A.480, A.482 Ligands: PGE.16 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:A.482, A.2

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

NAG.3: 7 residues within 4Å: Chain A: N.67, A.426, A.427, L.428, N.429, G.430 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.426, A:G.430 Water bridges: A:G.430

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

SO4.4: 1 residues within 4Å: Ligands: NAG.3 No protein-ligand interaction detected (PLIP) SO4.5: 4 residues within 4Å: Chain A: T.353, L.407, N.408, A.409 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.408, A:A.409 SO4.11: 5 residues within 4Å: Chain A: T.174, G.175, A.176, H.178, S.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.269, A:S.269 Salt bridges: A:H.178 SO4.17: 4 residues within 4Å: Chain A: R.346, V.359, N.450 Ligands: PEG.18 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.346, A:R.346, A:R.346, A:N.450, A:N.450 Salt bridges: A:R.346

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

LXE.6: 16 residues within 4Å: Chain A: F.93, C.160, C.161, D.163, D.173, M.179, W.190, D.203, E.205, N.206, N.207, L.208, G.279, G.280, D.281, S.283 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.205 Hydrogen bonds: A:D.163, A:E.205, A:N.206, A:N.207, A:N.207, A:G.280, A:D.281, A:D.281, A:D.281 Water bridges: A:S.283

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

ACT.7: 6 residues within 4Å: Chain A: R.226, V.319, L.322, N.382, Q.384 Ligands: PEG.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.319, A:Q.384 Hydrogen bonds: A:N.382 Water bridges: A:T.154, A:R.226, A:R.226, A:Q.384 Salt bridges: A:R.226 ACT.19: 3 residues within 4Å: Chain A: S.364, S.365, L.368 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.368 Hydrogen bonds: A:S.365

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

PEG.8: 8 residues within 4Å: Chain A: T.378, G.379, L.380, A.381, N.382, S.383, Q.384 Ligands: ACT.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.383, A:S.383 Water bridges: A:N.382 PEG.10: 6 residues within 4Å: Chain A: Y.26, S.28, F.29, S.30, Q.78, S.79 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.28 PEG.12: 10 residues within 4Å: Chain A: T.140, G.141, D.142, H.178, P.267, M.268, S.269, K.270, E.271 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.269 PEG.18: 8 residues within 4Å: Chain A: R.346, N.356, T.357, Q.358, E.449, N.450, V.451 Ligands: SO4.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.450 PEG.20: 5 residues within 4Å: Chain A: H.400, Y.401, N.402, F.403, Y.440 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.400, A:H.400, A:N.402, A:F.403 PEG.21: 8 residues within 4Å: Chain A: Y.343, T.357, H.447, Y.448, E.449, N.450, V.451, D.472 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.447, A:E.449, A:E.449, A:N.450, A:N.450 PEG.23: 7 residues within 4Å: Chain A: E.332, V.333, V.334, I.477, E.478, T.479, A.480 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.479, A:T.479 PEG.24: 2 residues within 4Å: Chain A: N.115, Q.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.117 PEG.25: 8 residues within 4Å: Chain A: D.94, G.95, P.96, D.97, T.98, D.99, G.100, V.460 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.100

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

PGE.9: 4 residues within 4Å: Chain A: A.32, T.46, Y.76, H.84 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.32 PGE.16: 5 residues within 4Å: Chain A: E.370, V.391, D.392, P.394 Ligands: ALA.2 1 PLIP interactions: 1 Ligand-Ligand interactions Hydrogen bonds: A.2 PGE.30: 8 residues within 4Å: Chain A: T.45, T.46, I.47, S.48, D.57, A.60, T.63, F.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.48, A:S.48, A:D.57

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

EDO.13: 4 residues within 4Å: Chain A: T.140, T.169, E.271 Ligands: PEG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.169 EDO.14: 5 residues within 4Å: Chain A: I.74, Y.76, H.84, T.86, N.132 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.132 EDO.15: 9 residues within 4Å: Chain A: S.210, G.211, A.212, N.217, S.218, G.219, D.220, Y.254, Y.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.218, A:S.218, A:G.219, A:Y.254 Water bridges: A:A.212 EDO.22: 4 residues within 4Å: Chain A: Y.448, Y.453, T.462, F.463 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.462 EDO.26: 5 residues within 4Å: Chain A: Q.35, Q.37, T.44, T.73, I.74 No protein-ligand interaction detected (PLIP) EDO.27: 5 residues within 4Å: Chain A: A.144, G.235, A.236, K.238, Y.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.236, A:K.238 Water bridges: A:A.144 EDO.28: 3 residues within 4Å: Chain A: N.410, D.411, G.412 No protein-ligand interaction detected (PLIP) EDO.29: 2 residues within 4Å: Chain A: T.51, A.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.52 EDO.31: 6 residues within 4Å: Chain A: T.188, Y.192, G.195, D.196, W.199 Ligands: NAG-NAG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.196 Water bridges: A:T.188

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
A

Alpha-L-arabinofuranosidase B