- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.64 Å
- Oligo State
- monomer
- Ligands
- 1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 3 x SO4: SULFATE ION(Non-functional Binders)
- 2 x ACT: ACETATE ION(Non-functional Binders)
ACT.4: 7 residues within 4Å:- Chain A: R.225, V.318, L.321, N.381, S.382, Q.383
- Ligands: PEG.14
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:V.318, A:Q.383
- Hydrogen bonds: A:N.381, A:Q.383
- Salt bridges: A:R.225
ACT.9: 4 residues within 4Å:- Chain A: L.379, N.409, G.411, H.416
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.409
- Salt bridges: A:H.416
- 3 x KHP: 4-nitrophenyl alpha-L-arabinofuranoside(Non-covalent)
KHP.5: 12 residues within 4Å:- Chain A: T.339, Y.342, T.356, R.445, H.446, Y.447, E.448, N.449, V.450, T.466, S.467, D.471
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:Y.447, A:E.448
- Hydrogen bonds: A:R.445, A:R.445, A:H.446, A:E.448, A:N.449, A:N.449, A:S.467, A:D.471
KHP.6: 10 residues within 4Å:- Chain A: R.398, H.399, Y.400, N.401, F.402, Q.414, D.418, Y.439
- Ligands: PEG.19, PGE.20
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:Y.400
- Hydrogen bonds: A:R.398, A:H.399, A:N.401, A:F.402, A:Q.414, A:D.418
- Water bridges: A:H.399
KHP.12: 17 residues within 4Å:- Chain A: F.92, C.159, C.160, D.162, D.172, M.178, W.189, D.202, M.203, Q.204, N.205, N.206, L.207, G.278, G.279, D.280, S.282
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:F.92, A:W.189
- Hydrogen bonds: A:Q.204, A:Q.204, A:N.205, A:N.206, A:N.206, A:G.279, A:D.280, A:D.280, A:S.282
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 5 residues within 4Å:- Chain A: Y.447, E.448, Y.452, T.461, F.462
No protein-ligand interaction detected (PLIP)EDO.10: 5 residues within 4Å:- Chain A: R.398, Y.400, L.405, N.407
- Ligands: SO4.3
3 PLIP interactions:3 interactions with chain A- Water bridges: A:R.398, A:N.407, A:N.407
EDO.11: 5 residues within 4Å:- Chain A: Y.25, S.27, F.28, Q.77, S.78
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.27
EDO.18: 4 residues within 4Å:- Chain A: T.353, E.403, V.450, Y.452
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:T.353, A:Y.452
EDO.21: 8 residues within 4Å:- Chain A: D.93, G.94, P.95, D.96, T.97, D.98, G.99, V.459
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:G.94, A:P.95
- Water bridges: A:D.98
EDO.22: 5 residues within 4Å:- Chain A: D.172, G.174, A.175, N.205
- Ligands: EDO.26
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.205
EDO.25: 3 residues within 4Å:- Chain A: T.187, Y.191, W.198
1 PLIP interactions:1 interactions with chain A- Water bridges: A:T.187
EDO.26: 6 residues within 4Å:- Chain A: D.172, T.173, G.174, N.205
- Ligands: EDO.22, PEG.23
No protein-ligand interaction detected (PLIP)EDO.27: 4 residues within 4Å:- Chain A: E.477, T.478, A.479, F.480
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.478
EDO.28: 5 residues within 4Å:- Chain A: P.340, G.341, Y.342, T.343, T.344
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:G.341, A:T.343, A:T.343, A:T.343
- Water bridges: A:G.341, A:T.344
EDO.30: 5 residues within 4Å:- Chain A: I.73, Y.75, H.83, T.85
- Ligands: 1PE.32
No protein-ligand interaction detected (PLIP)EDO.31: 6 residues within 4Å:- Chain A: Q.34, T.43, T.72, I.73, T.85
- Ligands: 1PE.32
1 PLIP interactions:1 interactions with chain A- Water bridges: A:T.72
EDO.33: 6 residues within 4Å:- Chain A: S.39, A.65, N.66, T.67, N.469
- Ligands: NAG.2
2 PLIP interactions:2 interactions with chain A- Water bridges: A:A.65, A:N.66
- 8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.13: 7 residues within 4Å:- Chain A: L.379, A.380, K.413, H.416, E.417
- Ligands: NAG-NAG.1, NAG-NAG.1
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.416
PEG.14: 8 residues within 4Å:- Chain A: T.377, G.378, L.379, A.380, N.381, S.382, Q.383
- Ligands: ACT.4
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.382, A:S.382
- Water bridges: A:R.225, A:N.381
PEG.15: 7 residues within 4Å:- Chain A: E.331, V.332, V.333, I.476, E.477, T.478, A.479
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:V.332
- Water bridges: A:V.332
PEG.16: 5 residues within 4Å:- Chain A: E.369, V.390, D.391, T.392, P.393
No protein-ligand interaction detected (PLIP)PEG.17: 8 residues within 4Å:- Chain A: R.345, N.355, T.356, Q.357, E.448, N.449, V.450
- Ligands: SO4.34
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:T.356
- Water bridges: A:R.345, A:R.345
PEG.19: 5 residues within 4Å:- Chain A: Y.400, N.401, E.403, F.462
- Ligands: KHP.6
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.401
PEG.23: 4 residues within 4Å:- Chain A: D.172, T.173
- Ligands: 1PE.24, EDO.26
No protein-ligand interaction detected (PLIP)PEG.29: 9 residues within 4Å:- Chain A: R.22, A.23, G.52, G.53, I.54, L.113, N.310, A.313, A.314
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.22, A:G.53, A:N.310
- Water bridges: A:N.310
- 1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.24: 7 residues within 4Å:- Chain A: T.139, T.168, S.169, T.173, K.269, E.270
- Ligands: PEG.23
No protein-ligand interaction detected (PLIP)1PE.32: 9 residues within 4Å:- Chain A: A.31, Q.34, T.43, T.45, I.73, Y.75, H.83
- Ligands: EDO.30, EDO.31
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.34
- Water bridges: A:A.31
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- McGregor, N.G.S. et al., Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining alpha-l-Arabinofuranosidases. J.Am.Chem.Soc. (2020)
- Release Date
- 2020-02-26
- Peptides
- Alpha-L-arabinofuranosidase B: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.64 Å
- Oligo State
- monomer
- Ligands
- 1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 3 x SO4: SULFATE ION(Non-functional Binders)
- 2 x ACT: ACETATE ION(Non-functional Binders)
- 3 x KHP: 4-nitrophenyl alpha-L-arabinofuranoside(Non-covalent)
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- McGregor, N.G.S. et al., Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining alpha-l-Arabinofuranosidases. J.Am.Chem.Soc. (2020)
- Release Date
- 2020-02-26
- Peptides
- Alpha-L-arabinofuranosidase B: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A