SMTL ID : 6zt9.1

X-ray structure of mutated arabinofuranosidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

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

AHR.1: 10 residues within 4Å: Chain A: F.26, E.28, G.73, C.74, E.176, Y.242, E.298, A.346, Q.347, M.352 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.28, A:C.74, A:E.298, A:Q.347 AHR.15: 10 residues within 4Å: Chain B: F.26, E.28, G.73, C.74, E.176, Y.242, E.298, A.346, Q.347, M.352 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.28, B:C.74, B:Y.242, B:E.298, B:Q.347 AHR.28: 11 residues within 4Å: Chain C: F.26, E.28, L.30, G.73, C.74, E.176, Y.242, E.298, A.346, Q.347, M.352 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.28, C:C.74, C:Y.242, C:Q.347 Water bridges: C:E.176, C:E.298 AHR.42: 10 residues within 4Å: Chain D: F.26, E.28, G.73, C.74, E.176, Y.242, E.298, A.346, Q.347, M.352 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.28, D:C.74, D:Y.242, D:E.298, D:Q.347 AHR.56: 10 residues within 4Å: Chain E: F.26, E.28, G.73, C.74, E.176, Y.242, E.298, A.346, Q.347, M.352 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.28, E:C.74, E:Y.242, E:E.298, E:Q.347 AHR.69: 11 residues within 4Å: Chain F: F.26, E.28, L.30, G.73, C.74, E.176, Y.242, E.298, A.346, Q.347, M.352 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:E.28, F:C.74, F:Y.242, F:Q.347 Water bridges: F:E.176, F:E.298

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

MPD.2: 4 residues within 4Å: Chain A: Y.220, E.224 Chain F: V.285, Y.286 Ligand excluded by PLIP MPD.3: 7 residues within 4Å: Chain A: M.114, E.118, G.121, C.122, E.123, P.124, R.167 Ligand excluded by PLIP MPD.4: 5 residues within 4Å: Chain A: R.20, K.64, K.376, Q.379, D.380 Ligand excluded by PLIP MPD.5: 5 residues within 4Å: Chain A: D.260, W.263, V.264, K.267, E.398 Ligand excluded by PLIP MPD.6: 5 residues within 4Å: Chain A: P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.7: 4 residues within 4Å: Chain A: P.152, N.155, W.156, E.159 Ligand excluded by PLIP MPD.8: 6 residues within 4Å: Chain A: R.194, K.228, Q.229, P.232, F.233 Chain C: R.185 Ligand excluded by PLIP MPD.9: 6 residues within 4Å: Chain A: K.15, R.335, H.336, C.337, D.338, L.383 Ligand excluded by PLIP MPD.16: 4 residues within 4Å: Chain B: Y.220, H.221, E.224 Chain E: V.285 Ligand excluded by PLIP MPD.17: 4 residues within 4Å: Chain B: K.15, K.290, R.335, D.338 Ligand excluded by PLIP MPD.18: 7 residues within 4Å: Chain B: M.114, C.117, E.118, G.121, C.122, P.124, R.167 Ligand excluded by PLIP MPD.19: 4 residues within 4Å: Chain B: D.260, W.263, V.264, E.398 Ligand excluded by PLIP MPD.20: 4 residues within 4Å: Chain B: K.64, K.376, V.377, Q.379 Ligand excluded by PLIP MPD.21: 7 residues within 4Å: Chain B: Q.197, K.210, P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.22: 7 residues within 4Å: Chain B: E.42, R.88, R.91, H.111, E.112, N.160, G.161 Ligand excluded by PLIP MPD.29: 5 residues within 4Å: Chain C: Y.220, H.221, E.224 Chain D: K.228, V.285 Ligand excluded by PLIP MPD.30: 4 residues within 4Å: Chain C: R.20, K.64, Q.379, D.380 Ligand excluded by PLIP MPD.31: 5 residues within 4Å: Chain C: D.260, W.263, V.264, K.267, E.398 Ligand excluded by PLIP MPD.32: 4 residues within 4Å: Chain C: R.194, K.228, Q.229, P.232 Ligand excluded by PLIP MPD.33: 7 residues within 4Å: Chain C: Q.197, K.210, P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.34: 9 residues within 4Å: Chain C: K.15, G.16, K.290, H.334, R.335, H.336, C.337, D.338, L.383 Ligand excluded by PLIP MPD.43: 4 residues within 4Å: Chain C: V.285, Y.286 Chain D: Y.220, E.224 Ligand excluded by PLIP MPD.44: 7 residues within 4Å: Chain D: M.114, E.118, G.121, C.122, E.123, P.124, R.167 Ligand excluded by PLIP MPD.45: 5 residues within 4Å: Chain D: R.20, K.64, K.376, Q.379, D.380 Ligand excluded by PLIP MPD.46: 5 residues within 4Å: Chain D: D.260, W.263, V.264, K.267, E.398 Ligand excluded by PLIP MPD.47: 5 residues within 4Å: Chain D: P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.48: 4 residues within 4Å: Chain D: P.152, N.155, W.156, E.159 Ligand excluded by PLIP MPD.49: 6 residues within 4Å: Chain D: R.194, K.228, Q.229, P.232, F.233 Chain F: R.185 Ligand excluded by PLIP MPD.50: 6 residues within 4Å: Chain D: K.15, R.335, H.336, C.337, D.338, L.383 Ligand excluded by PLIP MPD.57: 4 residues within 4Å: Chain B: V.285 Chain E: Y.220, H.221, E.224 Ligand excluded by PLIP MPD.58: 4 residues within 4Å: Chain E: K.15, K.290, R.335, D.338 Ligand excluded by PLIP MPD.59: 7 residues within 4Å: Chain E: M.114, C.117, E.118, G.121, C.122, P.124, R.167 Ligand excluded by PLIP MPD.60: 4 residues within 4Å: Chain E: D.260, W.263, V.264, E.398 Ligand excluded by PLIP MPD.61: 4 residues within 4Å: Chain E: K.64, K.376, V.377, Q.379 Ligand excluded by PLIP MPD.62: 7 residues within 4Å: Chain E: Q.197, K.210, P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.63: 7 residues within 4Å: Chain E: E.42, R.88, R.91, H.111, E.112, N.160, G.161 Ligand excluded by PLIP MPD.70: 5 residues within 4Å: Chain A: K.228, V.285 Chain F: Y.220, H.221, E.224 Ligand excluded by PLIP MPD.71: 4 residues within 4Å: Chain F: R.20, K.64, Q.379, D.380 Ligand excluded by PLIP MPD.72: 5 residues within 4Å: Chain F: D.260, W.263, V.264, K.267, E.398 Ligand excluded by PLIP MPD.73: 4 residues within 4Å: Chain F: R.194, K.228, Q.229, P.232 Ligand excluded by PLIP MPD.74: 7 residues within 4Å: Chain F: Q.197, K.210, P.232, F.233, M.234, H.235, R.291 Ligand excluded by PLIP MPD.75: 9 residues within 4Å: Chain F: K.15, G.16, K.290, H.334, R.335, H.336, C.337, D.338, L.383 Ligand excluded by PLIP

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

ACT.10: 5 residues within 4Å: Chain A: T.49, N.54, L.57, E.58, K.61 Ligand excluded by PLIP ACT.11: 5 residues within 4Å: Chain A: D.471, F.472, K.473, N.480, S.482 Ligand excluded by PLIP ACT.12: 4 residues within 4Å: Chain A: G.31, Y.35, V.102, I.103 Ligand excluded by PLIP ACT.13: 1 residues within 4Å: Chain A: N.373 Ligand excluded by PLIP ACT.23: 4 residues within 4Å: Chain B: T.49, L.57, E.58, K.61 Ligand excluded by PLIP ACT.24: 1 residues within 4Å: Chain B: M.153 Ligand excluded by PLIP ACT.25: 5 residues within 4Å: Chain B: D.471, F.472, K.473, N.480, S.482 Ligand excluded by PLIP ACT.26: 2 residues within 4Å: Chain B: V.102, I.103 Ligand excluded by PLIP ACT.27: 1 residues within 4Å: Chain B: P.466 Ligand excluded by PLIP ACT.35: 5 residues within 4Å: Chain C: W.39, G.41, E.42, R.88, H.107 Ligand excluded by PLIP ACT.36: 4 residues within 4Å: Chain C: T.49, L.57, E.58, K.61 Ligand excluded by PLIP ACT.37: 2 residues within 4Å: Chain C: P.152, W.156 Ligand excluded by PLIP ACT.38: 5 residues within 4Å: Chain C: D.471, F.472, K.473, N.480, S.482 Ligand excluded by PLIP ACT.39: 3 residues within 4Å: Chain C: G.31, V.102, I.103 Ligand excluded by PLIP ACT.40: 3 residues within 4Å: Chain C: K.164, P.165, R.167 Ligand excluded by PLIP ACT.41: 3 residues within 4Å: Chain C: N.373, M.374, P.466 Ligand excluded by PLIP ACT.51: 5 residues within 4Å: Chain D: T.49, N.54, L.57, E.58, K.61 Ligand excluded by PLIP ACT.52: 5 residues within 4Å: Chain D: D.471, F.472, K.473, N.480, S.482 Ligand excluded by PLIP ACT.53: 4 residues within 4Å: Chain D: G.31, Y.35, V.102, I.103 Ligand excluded by PLIP ACT.54: 1 residues within 4Å: Chain D: N.373 Ligand excluded by PLIP ACT.64: 4 residues within 4Å: Chain E: T.49, L.57, E.58, K.61 Ligand excluded by PLIP ACT.65: 1 residues within 4Å: Chain E: M.153 Ligand excluded by PLIP ACT.66: 5 residues within 4Å: Chain E: D.471, F.472, K.473, N.480, S.482 Ligand excluded by PLIP ACT.67: 2 residues within 4Å: Chain E: V.102, I.103 Ligand excluded by PLIP ACT.68: 1 residues within 4Å: Chain E: P.466 Ligand excluded by PLIP ACT.76: 5 residues within 4Å: Chain F: W.39, G.41, E.42, R.88, H.107 Ligand excluded by PLIP ACT.77: 4 residues within 4Å: Chain F: T.49, L.57, E.58, K.61 Ligand excluded by PLIP ACT.78: 2 residues within 4Å: Chain F: P.152, W.156 Ligand excluded by PLIP ACT.79: 5 residues within 4Å: Chain F: D.471, F.472, K.473, N.480, S.482 Ligand excluded by PLIP ACT.80: 3 residues within 4Å: Chain F: G.31, V.102, I.103 Ligand excluded by PLIP ACT.81: 3 residues within 4Å: Chain F: K.164, P.165, R.167 Ligand excluded by PLIP ACT.82: 3 residues within 4Å: Chain F: N.373, M.374, P.466 Ligand excluded by PLIP

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

BTB.14: 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.55: 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

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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