SMTL ID : 6zt7.1

X-ray structure of mutated arabinofuranosidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

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

ACT.1: 2 residues within 4Å: Chain A: N.373, P.466 Ligand excluded by PLIP ACT.2: 3 residues within 4Å: Chain A: D.148, R.158, E.163 Ligand excluded by PLIP ACT.3: 4 residues within 4Å: Chain A: T.49, N.54, L.57, E.58 Ligand excluded by PLIP ACT.4: 4 residues within 4Å: Chain A: W.387 Chain F: D.12, R.13 Ligands: ACT.5 Ligand excluded by PLIP ACT.5: 6 residues within 4Å: Chain A: R.6, V.8, W.387, E.388, S.389 Ligands: ACT.4 Ligand excluded by PLIP ACT.6: 5 residues within 4Å: Chain A: S.449, G.450, R.451, R.463, V.464 Ligand excluded by PLIP ACT.20: 3 residues within 4Å: Chain B: D.148, G.149, R.158 Ligand excluded by PLIP ACT.21: 5 residues within 4Å: Chain B: R.6, V.8, W.387, S.389 Ligands: ACT.23 Ligand excluded by PLIP ACT.22: 3 residues within 4Å: Chain B: T.49, E.58, K.61 Ligand excluded by PLIP ACT.23: 4 residues within 4Å: Chain B: W.387 Chain E: D.12, R.13 Ligands: ACT.21 Ligand excluded by PLIP ACT.24: 5 residues within 4Å: Chain B: S.449, G.450, R.451, R.463, V.464 Ligand excluded by PLIP ACT.34: 4 residues within 4Å: Chain C: W.39, G.41, E.42, R.88 Ligand excluded by PLIP ACT.35: 3 residues within 4Å: Chain C: T.49, N.54, E.58 Ligand excluded by PLIP ACT.36: 5 residues within 4Å: Chain C: R.194, K.228, Q.229, P.232, F.233 Ligand excluded by PLIP ACT.37: 4 residues within 4Å: Chain C: R.6, W.387, S.389 Ligands: ACT.38 Ligand excluded by PLIP ACT.38: 3 residues within 4Å: Chain C: R.6, E.432 Ligands: ACT.37 Ligand excluded by PLIP ACT.39: 5 residues within 4Å: Chain C: S.449, G.450, R.451, R.463, V.464 Ligand excluded by PLIP ACT.50: 2 residues within 4Å: Chain D: N.373, P.466 Ligand excluded by PLIP ACT.51: 3 residues within 4Å: Chain D: D.148, R.158, E.163 Ligand excluded by PLIP ACT.52: 4 residues within 4Å: Chain D: T.49, N.54, L.57, E.58 Ligand excluded by PLIP ACT.53: 4 residues within 4Å: Chain C: D.12, R.13 Chain D: W.387 Ligands: ACT.54 Ligand excluded by PLIP ACT.54: 6 residues within 4Å: Chain D: R.6, V.8, W.387, E.388, S.389 Ligands: ACT.53 Ligand excluded by PLIP ACT.55: 5 residues within 4Å: Chain D: S.449, G.450, R.451, R.463, V.464 Ligand excluded by PLIP ACT.69: 3 residues within 4Å: Chain E: D.148, G.149, R.158 Ligand excluded by PLIP ACT.70: 5 residues within 4Å: Chain E: R.6, V.8, W.387, S.389 Ligands: ACT.72 Ligand excluded by PLIP ACT.71: 3 residues within 4Å: Chain E: T.49, E.58, K.61 Ligand excluded by PLIP ACT.72: 4 residues within 4Å: Chain B: D.12, R.13 Chain E: W.387 Ligands: ACT.70 Ligand excluded by PLIP ACT.73: 5 residues within 4Å: Chain E: S.449, G.450, R.451, R.463, V.464 Ligand excluded by PLIP ACT.83: 4 residues within 4Å: Chain F: W.39, G.41, E.42, R.88 Ligand excluded by PLIP ACT.84: 3 residues within 4Å: Chain F: T.49, N.54, E.58 Ligand excluded by PLIP ACT.85: 5 residues within 4Å: Chain F: R.194, K.228, Q.229, P.232, F.233 Ligand excluded by PLIP ACT.86: 4 residues within 4Å: Chain F: R.6, W.387, S.389 Ligands: ACT.87 Ligand excluded by PLIP ACT.87: 3 residues within 4Å: Chain F: R.6, E.432 Ligands: ACT.86 Ligand excluded by PLIP ACT.88: 5 residues within 4Å: Chain F: S.449, G.450, R.451, R.463, V.464 Ligand excluded by PLIP

56 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 5 residues within 4Å: Chain A: K.15, R.335, C.337, D.338, L.383 Ligand excluded by PLIP MPD.8: 8 residues within 4Å: Chain A: M.114, C.117, E.118, G.121, C.122, E.123, P.124, R.167 Ligand excluded by PLIP MPD.9: 3 residues within 4Å: Chain A: R.20, K.64, D.380 Ligand excluded by PLIP MPD.10: 1 residues within 4Å: Chain A: F.271 Ligand excluded by PLIP MPD.11: 6 residues within 4Å: Chain A: D.260, W.263, V.264, K.267, P.395, E.398 Ligand excluded by PLIP MPD.12: 5 residues within 4Å: Chain A: K.61, E.118, L.119, L.120, G.121 Ligand excluded by PLIP MPD.13: 4 residues within 4Å: Chain A: R.32, T.309, F.313, Y.315 Ligand excluded by PLIP MPD.14: 6 residues within 4Å: Chain A: V.285, Y.286 Chain F: Y.220, H.221, E.224, I.282 Ligand excluded by PLIP MPD.15: 6 residues within 4Å: Chain A: K.210, P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.16: 4 residues within 4Å: Chain A: P.152, M.153, W.156, E.159 Ligand excluded by PLIP MPD.25: 5 residues within 4Å: Chain B: K.15, K.290, R.335, D.338, L.383 Ligand excluded by PLIP MPD.26: 2 residues within 4Å: Chain B: M.153, W.156 Ligand excluded by PLIP MPD.27: 3 residues within 4Å: Chain B: K.64, K.376, Q.379 Ligand excluded by PLIP MPD.28: 1 residues within 4Å: Chain B: R.32 Ligand excluded by PLIP MPD.29: 5 residues within 4Å: Chain B: P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.30: 5 residues within 4Å: Chain B: D.260, W.263, V.264, K.267, E.398 Ligand excluded by PLIP MPD.31: 2 residues within 4Å: Chain B: Y.241, F.271 Ligand excluded by PLIP MPD.32: 4 residues within 4Å: Chain B: Y.220, E.224, I.282 Chain E: V.285 Ligand excluded by PLIP MPD.33: 6 residues within 4Å: Chain B: K.61, K.64, E.118, L.119, L.120, G.121 Ligand excluded by PLIP MPD.40: 4 residues within 4Å: Chain C: V.285 Chain D: Y.220, H.221, E.224 Ligand excluded by PLIP MPD.41: 5 residues within 4Å: Chain C: K.15, K.290, R.335, D.338, L.383 Ligand excluded by PLIP MPD.42: 5 residues within 4Å: Chain C: R.20, K.64, K.376, Q.379, D.380 Ligand excluded by PLIP MPD.43: 4 residues within 4Å: Chain C: T.217, Y.241, K.268, F.271 Ligand excluded by PLIP MPD.44: 6 residues within 4Å: Chain C: Q.197, P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.45: 6 residues within 4Å: Chain C: D.260, W.263, V.264, K.267, P.395, E.398 Ligand excluded by PLIP MPD.46: 5 residues within 4Å: Chain C: K.61, E.118, L.119, L.120, G.121 Ligand excluded by PLIP MPD.47: 5 residues within 4Å: Chain C: R.162, K.164, P.165, W.166, R.167 Ligand excluded by PLIP MPD.48: 4 residues within 4Å: Chain C: P.152, M.153, W.156, E.159 Ligand excluded by PLIP MPD.56: 5 residues within 4Å: Chain D: K.15, R.335, C.337, D.338, L.383 Ligand excluded by PLIP MPD.57: 8 residues within 4Å: Chain D: M.114, C.117, E.118, G.121, C.122, E.123, P.124, R.167 Ligand excluded by PLIP MPD.58: 3 residues within 4Å: Chain D: R.20, K.64, D.380 Ligand excluded by PLIP MPD.59: 1 residues within 4Å: Chain D: F.271 Ligand excluded by PLIP MPD.60: 6 residues within 4Å: Chain D: D.260, W.263, V.264, K.267, P.395, E.398 Ligand excluded by PLIP MPD.61: 5 residues within 4Å: Chain D: K.61, E.118, L.119, L.120, G.121 Ligand excluded by PLIP MPD.62: 4 residues within 4Å: Chain D: R.32, T.309, F.313, Y.315 Ligand excluded by PLIP MPD.63: 6 residues within 4Å: Chain C: Y.220, H.221, E.224, I.282 Chain D: V.285, Y.286 Ligand excluded by PLIP MPD.64: 6 residues within 4Å: Chain D: K.210, P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.65: 4 residues within 4Å: Chain D: P.152, M.153, W.156, E.159 Ligand excluded by PLIP MPD.74: 5 residues within 4Å: Chain E: K.15, K.290, R.335, D.338, L.383 Ligand excluded by PLIP MPD.75: 2 residues within 4Å: Chain E: M.153, W.156 Ligand excluded by PLIP MPD.76: 3 residues within 4Å: Chain E: K.64, K.376, Q.379 Ligand excluded by PLIP MPD.77: 1 residues within 4Å: Chain E: R.32 Ligand excluded by PLIP MPD.78: 5 residues within 4Å: Chain E: P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.79: 5 residues within 4Å: Chain E: D.260, W.263, V.264, K.267, E.398 Ligand excluded by PLIP MPD.80: 2 residues within 4Å: Chain E: Y.241, F.271 Ligand excluded by PLIP MPD.81: 4 residues within 4Å: Chain B: V.285 Chain E: Y.220, E.224, I.282 Ligand excluded by PLIP MPD.82: 6 residues within 4Å: Chain E: K.61, K.64, E.118, L.119, L.120, G.121 Ligand excluded by PLIP MPD.89: 4 residues within 4Å: Chain A: Y.220, H.221, E.224 Chain F: V.285 Ligand excluded by PLIP MPD.90: 5 residues within 4Å: Chain F: K.15, K.290, R.335, D.338, L.383 Ligand excluded by PLIP MPD.91: 5 residues within 4Å: Chain F: R.20, K.64, K.376, Q.379, D.380 Ligand excluded by PLIP MPD.92: 4 residues within 4Å: Chain F: T.217, Y.241, K.268, F.271 Ligand excluded by PLIP MPD.93: 6 residues within 4Å: Chain F: Q.197, P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.94: 6 residues within 4Å: Chain F: D.260, W.263, V.264, K.267, P.395, E.398 Ligand excluded by PLIP MPD.95: 5 residues within 4Å: Chain F: K.61, E.118, L.119, L.120, G.121 Ligand excluded by PLIP MPD.96: 5 residues within 4Å: Chain F: R.162, K.164, P.165, W.166, R.167 Ligand excluded by PLIP MPD.97: 4 residues within 4Å: Chain F: P.152, M.153, W.156, E.159 Ligand excluded by PLIP

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.17: 6 residues within 4Å: Chain A: G.86, P.87, R.88, R.91, E.112, N.160 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.88, A:R.88, A:E.112, A:N.160 BTB.66: 6 residues within 4Å: Chain D: G.86, P.87, R.88, R.91, E.112, N.160 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.88, D:R.88, D:E.112, D:E.112, D:N.160

6 x AHR: alpha-L-arabinofuranose(Non-covalent)

AHR.18: 8 residues within 4Å: Chain A: E.28, L.30, G.73, C.74, E.176, Y.242, E.298, W.302 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.28, A:C.74, A:E.298 Water bridges: A:F.75, A:F.75, A:E.176 AHR.19: 8 residues within 4Å: Chain B: E.28, L.30, G.73, C.74, E.176, Y.242, E.298, W.302 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.28, B:C.74, B:E.298 Water bridges: B:F.75 AHR.49: 8 residues within 4Å: Chain C: E.28, L.30, G.73, C.74, E.176, Y.242, E.298, W.302 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.28, C:C.74, C:Y.242, C:E.298 AHR.67: 8 residues within 4Å: Chain D: E.28, L.30, G.73, C.74, E.176, Y.242, E.298, W.302 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.28, D:C.74, D:Y.242, D:E.298 Water bridges: D:F.75, D:F.75 AHR.68: 8 residues within 4Å: Chain E: E.28, L.30, G.73, C.74, E.176, Y.242, E.298, W.302 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.28, E:C.74, E:Y.242, E:E.298 Water bridges: E:F.75 AHR.98: 8 residues within 4Å: Chain F: E.28, L.30, G.73, C.74, E.176, Y.242, E.298, W.302 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.28, F:C.74, F:E.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, J. et al., Probing the determinants of the transglycosylation/hydrolysis partition in a retaining alpha-l-arabinofuranosidase. N Biotechnol (2021)

Release Date

2021-02-10

Peptides

Alpha-L-arabinofuranosidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Alpha-L-arabinofuranosidase

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