SMTL ID : 6md6.1

CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE IN COMPLEX WITH METHYL 2-THIO-BETA-SOPHOROSIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

1 x U2A- BGC: beta-D-glucopyranose-(1-2)-methyl 2-thio-beta-D-glucopyranoside(Non-covalent)

U2A-BGC.1: 10 residues within 4Å: Chain A: G.60, G.61, W.290, E.291, N.323, W.434, W.438, E.495 Ligands: GOL.5, 1PE.22 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.61, A:G.61, A:G.61, A:Y.257, A:R.295 Water bridges: A:R.295, A:R.295, A:W.290, A:N.323, A:N.323

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

NAG.2: 7 residues within 4Å: Chain A: E.224, N.225, N.226, S.259, K.264 Ligands: GOL.13, 1PE.18 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.226 Hydrogen bonds: A:K.264 Water bridges: A:N.225, A:N.225, A:N.225 NAG.3: 4 residues within 4Å: Chain A: D.499, N.500, N.502 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.499 Water bridges: A:N.500, A:L.501, A:N.502 NAG.4: 1 residues within 4Å: Chain A: N.604 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.604 Water bridges: A:N.604, A:N.604

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: D.99, F.148, R.162, K.210, H.211, M.254, D.289, W.434 Ligands: U2A-BGC.1, 1PE.22 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.162, A:R.162, A:K.210 Water bridges: A:D.99 GOL.6: 3 residues within 4Å: Chain A: R.26, M.27, T.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.26 Water bridges: A:L.29, A:R.89, A:R.89 GOL.7: 5 residues within 4Å: Chain A: Q.379, R.382, G.448, T.449, E.553 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.448, A:T.449, A:T.449 Water bridges: A:Q.379, A:Q.555, A:Q.555, A:Q.555 GOL.8: 5 residues within 4Å: Chain A: F.467, A.468, E.469, N.470, P.471 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.469, A:N.470, A:N.470 Water bridges: A:F.467, A:E.469, A:N.470 GOL.9: 2 residues within 4Å: Chain A: R.390, K.391 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.390, A:R.390, A:K.391 Water bridges: A:R.130, A:R.130, A:E.387, A:K.391 GOL.10: 3 residues within 4Å: Chain A: T.298, P.299, A.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.298, A:A.300 GOL.11: 4 residues within 4Å: Chain A: R.123, I.173, L.597, G.598 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.123, A:R.570 GOL.12: 10 residues within 4Å: Chain A: R.156, D.157, P.158, E.169, R.573, T.574, L.582, P.583, M.584, N.585 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.169, A:R.573, A:T.574, A:M.584, A:N.585 GOL.13: 5 residues within 4Å: Chain A: G.262, K.264, I.296, T.298 Ligands: NAG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.264, A:I.296, A:T.298, A:T.298 Water bridges: A:S.259 GOL.14: 7 residues within 4Å: Chain A: H.491, Y.493, K.497, G.498, N.500, R.530 Ligands: NAG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.498, A:N.500, A:R.530 Water bridges: A:H.491, A:K.497

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

SO4.15: 3 residues within 4Å: Chain A: P.342, M.343, S.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.343, A:S.344 SO4.16: 5 residues within 4Å: Chain A: Q.175, T.178, E.179, N.244, K.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.179, A:N.244 Salt bridges: A:K.248

6 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 1PE.18: 3 residues within 4Å: Chain A: N.226, I.228 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.226 1PE.19: 2 residues within 4Å: Chain A: Y.306, K.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.306 1PE.20: 4 residues within 4Å: Chain A: L.594, F.595, R.596, Y.599 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.596, A:R.596 1PE.21: 3 residues within 4Å: Chain A: E.374, K.378, E.380 No protein-ligand interaction detected (PLIP) 1PE.22: 10 residues within 4Å: Chain A: L.58, D.99, R.162, K.210, H.211, M.254, D.289, M.320 Ligands: U2A-BGC.1, GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.210 Water bridges: A:R.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Streltsov, V.A. et al., Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site. Nat Commun (2019)

Release Date

2019-05-29

Peptides

Beta-D-glucan exohydrolase isoenzyme ExoI: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-D-glucan exohydrolase isoenzyme ExoI

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