SMTL ID : 3wli.1

Crystal Structure Analysis of Plant Exohydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: E.224, N.225, N.226, S.259, K.264 6 PLIP interactions: 6 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, A:T.298 NAG.2: 2 residues within 4Å: Chain A: T.602, N.604 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: D.499, N.500, N.502 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.499 Water bridges: A:L.501, A:N.502, A:N.502

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: A.200, G.201, K.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.202 Water bridges: A:N.365 GOL.5: 3 residues within 4Å: Chain A: P.411, K.412, K.413 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.412, A:K.413, A:K.413 GOL.6: 4 residues within 4Å: Chain A: E.387, R.390, K.391, F.565 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.390, A:R.390, A:K.391 Water bridges: A:K.391 GOL.7: 2 residues within 4Å: Chain A: F.192, D.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.192 Water bridges: A:F.192, A:S.194, A:S.194 GOL.8: 5 residues within 4Å: Chain A: Q.439, G.440, D.441, H.491, P.492 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.440 Water bridges: A:D.441, A:H.491 GOL.9: 2 residues within 4Å: Chain A: R.171, R.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.171, A:R.171 Water bridges: A:Q.175 GOL.10: 9 residues within 4Å: Chain A: L.58, D.99, M.254, D.289, W.290, M.320, W.434, E.495 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.289, A:E.495 Water bridges: A:R.162 GOL.11: 3 residues within 4Å: Chain A: G.61 Ligands: GOL.12, GOL.13 No protein-ligand interaction detected (PLIP) GOL.12: 8 residues within 4Å: Chain A: G.60, G.61, W.290, W.434, W.438 Ligands: GOL.10, GOL.11, GOL.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.61 Water bridges: A:W.290 GOL.13: 6 residues within 4Å: Chain A: G.60, G.61, W.290, W.438 Ligands: GOL.11, GOL.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.61 GOL.14: 4 residues within 4Å: Chain A: T.298, P.299, A.300 Ligands: SO4.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.300 Water bridges: A:T.298 GOL.15: 3 residues within 4Å: Chain A: P.342, M.343, S.344 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.343, A:S.344, A:S.344 Water bridges: A:S.344 GOL.16: 4 residues within 4Å: Chain A: S.305, K.309, H.335 Ligands: SO4.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.305, A:S.305, A:K.309

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

SO4.17: 4 residues within 4Å: Chain A: A.468, E.469, N.470, P.471 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.469, A:N.470, A:N.470 Water bridges: A:D.472 SO4.18: 5 residues within 4Å: Chain A: P.593, L.594, F.595, R.596, Y.599 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.596, A:R.596 SO4.19: 4 residues within 4Å: Chain A: T.298, P.299, A.300 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.300 Water bridges: A:A.300 SO4.20: 4 residues within 4Å: Chain A: K.309, H.335, V.340 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.309, A:K.309 Salt bridges: A:K.309

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

2015-03-25

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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