SMTL ID : 7mgu.1

Improved ligand discovery using micro-beam data collection at the edge of protein crystals

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x ARG: ARGININE(Non-covalent)

ARG.1: 11 residues within 4Å: Chain A: W.18, N.44, V.46, Y.77, W.79, E.86, Y.88, P.126, S.127, I.128, E.177 16 PLIP interactions: 15 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.18 Hydrogen bonds: A:N.44, A:N.44, A:Y.77, A:Y.88, A:Y.88, A:S.127 Water bridges: A:R.122, A:R.122, A:S.127, A:Q.136, A:Q.136, A:Q.136, R.1 Salt bridges: A:E.86, A:E.177

5 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: W.79, Y.87, M.169, D.170, Y.171, Q.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.79, A:Y.87, A:D.170, A:D.170 NA.3: 5 residues within 4Å: Chain A: S.110, D.111, Y.115, V.150, H.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.111, A:Y.115 NA.4: 6 residues within 4Å: Chain A: V.46, Y.77, Y.88, A.175, E.177 Ligands: NA.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.88 NA.5: 6 residues within 4Å: Chain A: N.71, S.72, Y.73, G.94, T.95, Y.96 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.71, A:S.72, A:G.94, A:Y.96 NA.6: 5 residues within 4Å: Chain A: Y.73, S.75, A.175, E.177 Ligands: NA.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.175, A:E.177

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

EDO.7: 5 residues within 4Å: Chain A: R.81, N.82, P.83, L.84, I.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.82, A:N.82 Water bridges: A:N.82 EDO.8: 2 residues within 4Å: Chain A: N.124, T.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.124, A:N.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soares, A.S. et al., Improved ligand discovery using micro-beam data collection at the edge of protein crystals. To Be Published

Release Date

2021-09-08

Peptides

Endo-1,4-beta-xylanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endo-1,4-beta-xylanase

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