SMTL ID : 6lc5.1

Crystal structure of barley exohydrolaseI W434F in complex with 4'-nitrophenyl thiolaminaribioside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

1 x 6BV: (2~{R},3~{S},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanyl-oxane-2,3,5-triol(Non-covalent)

6BV.1: 15 residues within 4Å: Chain A: L.58, 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 Ligands: GOL.15 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.162, A:R.162, A:K.210, A:R.295, A:R.295 Water bridges: A:G.61, A:G.61, A:G.61, A:K.210 Salt bridges: A:R.295

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

1PE.2: 5 residues within 4Å: Chain A: D.5, Y.6, V.7, K.10, D.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.7 Water bridges: A:A.12 1PE.3: 4 residues within 4Å: Chain A: G.399, K.400, T.401, S.402 No protein-ligand interaction detected (PLIP) 1PE.4: 4 residues within 4Å: Chain A: P.15, V.16, E.17 Ligands: 1PE.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.16, A:E.17 Water bridges: A:E.17, A:E.17 1PE.5: 3 residues within 4Å: Chain A: T.28, A.30, F.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.28 1PE.6: 2 residues within 4Å: Chain A: R.390, K.391 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.390, A:R.390, A:K.391 1PE.7: 3 residues within 4Å: Chain A: E.17, K.283 Ligands: 1PE.4 No protein-ligand interaction detected (PLIP) 1PE.8: 4 residues within 4Å: Chain A: R.123, P.125, I.173, S.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.176 1PE.9: 5 residues within 4Å: Chain A: G.587, D.588, A.589 Ligands: EPE.22, ACT.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.589 Water bridges: A:H.590 1PE.10: 4 residues within 4Å: Chain A: T.297, T.298, D.303, Y.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.298, A:D.303 1PE.11: 4 residues within 4Å: Chain A: D.170, R.171, R.172, V.586 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.171 1PE.12: 3 residues within 4Å: Chain A: Q.379, E.380, D.383 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 5 residues within 4Å: Chain A: T.504, I.505, V.533, P.536, L.537 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.505, A:L.537 GOL.14: 4 residues within 4Å: Chain A: G.25, R.26, M.27, T.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.27 GOL.15: 10 residues within 4Å: Chain A: W.160, R.162, H.211, D.215, S.256, Y.257, S.258, D.289, E.495 Ligands: 6BV.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.162, A:Y.257, A:S.258, A:D.289, A:D.289, A:E.495 GOL.16: 5 residues within 4Å: Chain A: Q.379, R.382, G.448, T.449, E.553 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.449, A:T.449, A:S.552 Water bridges: A:Q.379, A:Q.379, A:R.382, A:Q.555, A:Q.555, A:Q.555

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

SO4.17: 3 residues within 4Å: Chain A: A.200, G.201, K.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.202, A:N.203 Water bridges: A:A.200, A:N.203 Salt bridges: A:K.202 SO4.18: 3 residues within 4Å: Chain A: E.291, N.323, K.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.323 Water bridges: A:N.323 Salt bridges: A:K.324 SO4.19: 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

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.20: 7 residues within 4Å: Chain A: Y.126, R.130, E.133, E.380, H.381, L.384 Ligands: ACT.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.126, A:H.381 EPE.21: 7 residues within 4Å: Chain A: R.171, R.172, Q.175, S.176, T.178, N.244, K.248 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.171, A:R.171, A:Q.175, A:N.244 Water bridges: A:Q.175 Salt bridges: A:K.248 EPE.22: 8 residues within 4Å: Chain A: R.156, T.218, P.583, N.585, V.586, G.587, D.588 Ligands: 1PE.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.156, A:N.585 Water bridges: A:T.218, A:T.218 Salt bridges: A:R.156, A:D.588

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

ACT.23: 3 residues within 4Å: Chain A: L.137, H.381 Ligands: EPE.20 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.381 ACT.24: 1 residues within 4Å: Ligands: 1PE.9 No protein-ligand interaction detected (PLIP)

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

2020-09-30

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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