SMTL ID : 6sxv.1 (1 other biounit)

GH51 a-l-arabinofuranosidase soaked with aziridine inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

LXE.1: 17 residues within 4Å: Chain A: F.27, E.29, L.31, G.73, N.74, W.99, N.174, E.175, H.244, Y.246, E.294, L.318, A.350, Q.351, V.355, I.356 Ligands: GOL.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.294 Hydrogen bonds: A:E.29, A:G.73, A:N.74, A:N.174, A:H.244, A:Q.351 Water bridges: A:N.74, A:E.175, A:E.175, A:E.175, A:E.294, A:E.294

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: H.184, K.185, E.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.189 Water bridges: A:E.189 GOL.5: 6 residues within 4Å: Chain A: W.99, Y.246, W.298, L.318, I.356 Ligands: LXE.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.74, A:N.74, A:N.74 GOL.6: 4 residues within 4Å: Chain A: I.157, A.158, H.159, G.160 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.157 GOL.7: 8 residues within 4Å: Chain A: G.248, N.249, R.250, D.251, D.253, N.256, Y.257, L.260 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.249, A:R.250, A:D.251, A:D.251, A:N.256 Water bridges: A:G.248, A:R.250 GOL.8: 1 residues within 4Å: Chain A: W.203 No protein-ligand interaction detected (PLIP)

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

PEG.3: 8 residues within 4Å: Chain A: A.98, W.99, K.100, D.305, I.308, E.309, P.310, L.317 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.98, A:I.308

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

PGE.4: 3 residues within 4Å: Chain A: H.184, T.186, E.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.184, A:E.189 Water bridges: A:T.186, A:T.186

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

GH51 a-l-arabinofuranosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GH51 a-l-arabinofuranosidase

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