SMTL ID : 3ug3.1

Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima ligand free form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 7 residues within 4Å: Chain A: N.95, R.111, F.112, L.114 Chain B: D.152, L.155, H.156 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:L.155 Hydrogen bonds: A:N.95, A:R.111, A:F.112, A:F.112 TRS.13: 7 residues within 4Å: Chain B: N.95, R.111, F.112, L.114 Chain C: D.152, L.155, H.156 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.95, B:R.111, B:F.112 Water bridges: B:F.112, C:L.155 TRS.22: 7 residues within 4Å: Chain A: D.152, L.155, H.156 Chain C: N.95, R.111, F.112, L.114 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.95, C:R.111, C:F.112 Water bridges: C:F.112 TRS.40: 7 residues within 4Å: Chain D: N.95, R.111, F.112, L.114 Chain F: D.152, L.155, H.156 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:N.95, D:R.111, D:F.112 Water bridges: F:L.155 TRS.41: 7 residues within 4Å: Chain D: D.152, L.155, H.156 Chain E: N.95, R.111, F.112, L.114 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain E Water bridges: D:L.155 Hydrogen bonds: E:N.95, E:R.111, E:F.112, E:F.112 TRS.50: 7 residues within 4Å: Chain E: D.152, L.155, H.156 Chain F: N.95, R.111, F.112, L.114 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain F Water bridges: E:L.155, F:F.112 Hydrogen bonds: F:N.95, F:R.111, F:F.112

51 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 11 residues within 4Å: Chain A: F.44, E.46, L.48, N.91, W.116, Y.257, E.301, W.305, L.313, Q.346, L.351 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: E.192, W.197, Y.257 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: H.255, F.256, Y.257, M.397, F.398 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: R.209, E.213 Chain C: G.200, H.201 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: V.33, K.334, L.381, V.382, K.383, T.384 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: V.220, F.221 Chain C: F.112, Q.117 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: Y.264, Y.391, F.411 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: K.216, W.217, V.220 Chain C: E.196, W.197 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: E.275, I.278 Chain D: K.281, K.282 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: G.200, H.201 Chain B: R.209, E.213 Ligand excluded by PLIP EDO.14: 10 residues within 4Å: Chain B: F.44, E.46, L.48, W.116, Y.257, E.301, W.305, L.313, Q.346, L.351 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: E.192, W.197, Y.257 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: H.255, F.256, Y.257, M.397, F.398, M.402 Ligands: EDO.15 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: V.33, K.334, L.381, V.382, K.383, T.384 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: N.162, K.164, F.221, D.222 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: Y.264, Y.391, N.392, F.411 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: W.197 Chain B: K.216, W.217, V.220 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: L.114, A.115, Q.117, W.197 Chain C: W.217 Ligand excluded by PLIP EDO.23: 12 residues within 4Å: Chain C: F.44, E.46, L.48, N.91, W.116, Y.257, E.301, W.305, L.313, A.345, Q.346, L.351 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain C: E.192, W.197, H.255, Y.257 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain C: H.255, F.256, Y.257, M.397, F.398, M.402 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: G.200, H.201 Chain C: R.209, E.213 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain C: V.33, L.381, V.382, K.383, T.384 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain C: N.162, K.164, F.221, D.222 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain C: Y.264, Y.391, F.411 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: E.275, I.278 Chain F: I.278, K.281, K.282 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain D: L.48, N.91, W.116, Y.257, E.301, W.305, L.313, Q.346, L.351 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain D: E.192, W.197, Y.257 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain D: H.255, F.256, Y.257, M.397, F.398 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain D: R.209, E.213 Chain E: G.200, H.201 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain D: V.33, K.334, L.381, V.382, K.383, T.384 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain D: N.162, K.164, F.221, D.222 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain D: Y.264, Y.391, N.392, F.411 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain D: K.216, W.217, V.220 Chain E: W.197 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain A: K.281, K.282 Chain D: E.275 Ligand excluded by PLIP EDO.42: 10 residues within 4Å: Chain E: F.44, E.46, L.48, W.116, Y.257, E.301, W.305, L.313, Q.346, L.351 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain E: E.192, W.197, Y.257 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain E: H.255, F.256, Y.257, M.397, F.398 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain E: R.209, E.213 Chain F: G.200, H.201 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain E: V.33, K.334, L.381, K.383, T.384 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain E: N.162, K.164, F.221, D.222 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain E: Y.264, Y.391, F.411 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain E: K.216, W.217, V.220 Chain F: E.196, W.197 Ligand excluded by PLIP EDO.51: 11 residues within 4Å: Chain F: F.44, E.46, L.48, N.91, W.116, Y.257, E.301, W.305, L.313, Q.346, L.351 Ligand excluded by PLIP EDO.52: 4 residues within 4Å: Chain F: E.192, W.197, Y.257, F.398 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain F: H.255, F.256, Y.257, M.397, F.398, M.402 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain D: G.200, H.201 Chain F: R.209, E.213 Ligand excluded by PLIP EDO.55: 6 residues within 4Å: Chain F: V.33, K.334, L.381, V.382, K.383, T.384 Ligand excluded by PLIP EDO.56: 4 residues within 4Å: Chain F: N.162, K.164, F.221, D.222 Ligand excluded by PLIP EDO.57: 3 residues within 4Å: Chain F: Y.264, Y.391, F.411 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain D: E.196, W.197 Chain F: W.217 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 2 residues within 4Å: Chain A: P.223, K.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.226, A:K.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Im, D.-H. et al., Crystal Structures of Glycoside Hydrolase Family 51 alpha-L-Arabinofuranosidase from Thermotoga maritima. Biosci.Biotechnol.Biochem. (2012)

Release Date

2012-03-07

Peptides

Alpha-L-arabinofuranosidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Alpha-L-arabinofuranosidase

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