SMTL ID : 6jgk.1

Crystal structure of barley exohydrolaseI W434F mutant in complex with 4I,4III,4V-S-trithiocellohexaose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

1 x GS1- SGC- BGC: beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-1-thio-beta-D-glucopyranose

GS1-SGC-BGC.1: 18 residues within 4Å: Chain A: L.58, G.60, G.61, D.99, F.148, R.162, K.210, H.211, M.254, Y.257, D.289, W.290, R.295, M.320, W.434, F.438, E.495 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.162, A:R.162, A:K.210, A:H.211, A:H.211, A:R.295, A:G.61, A:Y.257, A:R.295, A:R.295 Water bridges: A:K.210, A:R.295

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

NAG.2: 1 residues within 4Å: Chain A: N.604 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.604 Water bridges: A:N.604 NAG.3: 4 residues within 4Å: Chain A: D.499, N.500, N.502, T.504 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.499, A:N.502, A:T.504 Water bridges: A:L.501, A:L.503, A:L.503 NAG.4: 5 residues within 4Å: Chain A: E.224, N.225, N.226, S.259, K.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.264 Water bridges: A:N.225, A:N.225, A:N.225

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.123, I.173, R.570, L.597, G.598 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.123, A:R.570, A:R.570 GOL.6: 11 residues within 4Å: Chain A: W.160, R.162, H.211, D.215, N.223, E.224, S.256, Y.257, S.258, D.289 Ligands: GS1-SGC-BGC.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.162, A:N.223, A:E.224, A:Y.257, A:S.258, A:D.289, A:D.289 GOL.7: 4 residues within 4Å: Chain A: G.25, R.26, M.27, T.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.27 Water bridges: A:R.26 GOL.8: 7 residues within 4Å: Chain A: Y.429, Q.439, G.440, D.441, T.442, H.491, P.492 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.429, A:Y.429 Water bridges: A:T.442 GOL.9: 3 residues within 4Å: Chain A: A.200, G.201, K.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.202 Water bridges: A:K.202, A:N.365 GOL.10: 5 residues within 4Å: Chain A: Q.379, R.382, G.448, T.449, E.553 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.449, A:T.449, A:S.552 Water bridges: A:Q.379, A:R.382, A:E.553, A:Q.555, A:Q.555

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

SO4.11: 3 residues within 4Å: Chain A: R.171, R.172, N.236 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.236 Water bridges: A:R.171, A:R.171 Salt bridges: A:R.171, A:R.172 SO4.12: 4 residues within 4Å: Chain A: T.297, T.298, P.299, A.300 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.300 SO4.13: 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 SO4.14: 2 residues within 4Å: Chain A: R.171, R.172 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.175, A:Q.175 Salt bridges: A:R.171

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

1PE.15: 5 residues within 4Å: Chain A: Q.175, S.176, T.178, N.244, K.248 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.244, A:K.248, A:K.248 Water bridges: A:S.176 1PE.16: 2 residues within 4Å: Chain A: K.281, K.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.283 Water bridges: A:D.278, A:K.283 1PE.17: 3 residues within 4Å: Chain A: D.588, A.589, H.590 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.589, A:H.590 Water bridges: A:H.590 1PE.18: 3 residues within 4Å: Chain A: P.15, V.16, E.17 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.16, A:E.17 Water bridges: A:E.17, A:E.17, A:E.17, A:E.17 1PE.19: 1 residues within 4Å: Chain A: K.416 No protein-ligand interaction detected (PLIP) 1PE.20: 6 residues within 4Å: Chain A: H.491, Y.493, K.497, G.498, N.500, R.530 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.498, A:N.500, A:R.530 Water bridges: A:H.491 1PE.21: 3 residues within 4Å: Chain A: P.411, K.412, K.413 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.412, A:K.413, A:K.413 Water bridges: A:L.410, A:F.562 1PE.22: 5 residues within 4Å: Chain A: A.468, E.469, N.470, P.471, F.475 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.469, A:N.470 1PE.23: 2 residues within 4Å: Chain A: R.386, Q.555 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.386, A:R.386 Water bridges: A:Q.555 1PE.24: 3 residues within 4Å: Chain A: K.397, K.400, A.539 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.397, A:K.400, A:A.539 Water bridges: A:K.400 1PE.25: 3 residues within 4Å: Chain A: E.387, R.390, K.391 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.390, A:R.390, A:K.391 Water bridges: A:R.130, A:R.130

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

ACT.26: 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 Salt bridges: A:R.596 ACT.27: 3 residues within 4Å: Chain A: G.109, L.376, R.382 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.376, A:R.382 ACT.28: 2 residues within 4Å: Chain A: N.604, A.605 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.566, A:A.605 ACT.29: 3 residues within 4Å: Chain A: E.17, M.196, K.283 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.17 Salt bridges: A:R.355

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luang, S. et al., The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases. Nat Commun (2022)

Release Date

2020-08-19

Peptides

Uncharacterized protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uncharacterized protein

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