SMTL ID : 4nzf.1 (1 other biounit)

Crystal structure of Abp-D197A (a GH27-b-L-arabinopyranosidase from Geobacillus stearothermophilus), in complex with arabinose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-tetramer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: W.161, D.254, D.255 Ligands: ARB.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.254, A:D.255 Water bridges: A:Y.79 GOL.16: 4 residues within 4Å: Chain B: W.161, D.254, D.255 Ligands: ARB.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.255 Water bridges: B:D.299 GOL.17: 4 residues within 4Å: Chain B: S.398, K.400, D.401, H.424 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.398, B:S.398 GOL.18: 7 residues within 4Å: Chain B: K.172, E.173, G.174, A.175, Q.176, A.177 Ligands: SO4.29 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.170, B:G.174, B:A.175, B:Q.176, B:A.177 GOL.35: 4 residues within 4Å: Chain C: W.161, D.254, D.255 Ligands: ARB.40 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.254 Water bridges: C:Y.79 GOL.36: 2 residues within 4Å: Chain C: K.217, R.221 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.221, C:R.221 GOL.37: 6 residues within 4Å: Chain C: K.275 Chain D: A.14, S.15, Y.19, V.244, H.281 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.14, D:S.15 Water bridges: D:S.15 GOL.38: 2 residues within 4Å: Chain C: K.53, Y.54 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.53, C:Y.54 GOL.39: 8 residues within 4Å: Chain C: H.170, K.172, E.173, G.174, A.175, Q.176, A.177 Ligands: SO4.44 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.170, C:G.174, C:G.174, C:A.175, C:Q.176, C:A.177 GOL.54: 5 residues within 4Å: Chain D: W.161, P.232, D.254, D.255 Ligands: ARB.57 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.255 GOL.55: 5 residues within 4Å: Chain D: L.421, V.422, K.423, H.424, Q.425 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.421, D:K.423, D:H.424, D:Q.425 GOL.56: 7 residues within 4Å: Chain D: H.170, K.172, G.174, A.175, Q.176, A.177 Ligands: SO4.66 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.174, D:A.175, D:Q.176, D:A.177 Water bridges: D:R.221

4 x ARB: beta-L-arabinopyranose(Non-covalent)

ARB.2: 13 residues within 4Å: Chain A: W.32, D.66, Y.79, H.126, W.161, K.195, A.197, S.231, P.232, R.251, D.255, M.287 Ligands: GOL.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.195, A:K.195, A:R.251, A:R.251 Water bridges: A:K.195, A:D.255, A:D.286, A:D.286 Salt bridges: A:H.126, A:K.195 ARB.19: 14 residues within 4Å: Chain B: W.32, D.66, I.67, Y.79, H.126, W.161, K.195, A.197, S.231, P.232, R.251, D.255, M.287 Ligands: GOL.16 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.195, B:K.195, B:S.231, B:R.251, B:R.251, B:D.255 Salt bridges: B:H.126 ARB.40: 13 residues within 4Å: Chain C: W.32, D.66, Y.79, H.126, W.161, K.195, A.197, S.231, P.232, R.251, D.255, M.287 Ligands: GOL.35 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:K.195, C:K.195, C:S.231, C:S.231, C:R.251, C:R.251, C:D.255 Salt bridges: C:H.126, C:K.195 ARB.57: 13 residues within 4Å: Chain D: W.32, D.66, Y.79, H.126, W.161, K.195, A.197, S.231, P.232, R.251, D.255, M.287 Ligands: GOL.54 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:K.195, D:K.195, D:S.231, D:R.251, D:R.251, D:D.255 Salt bridges: D:H.126, D:K.195

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

SO4.3: 3 residues within 4Å: Chain A: H.17, W.21, P.225 Ligand excluded by PLIP SO4.4: 1 residues within 4Å: Chain A: R.80 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: H.117, R.224 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: E.173, G.174, A.175, Q.176, A.177 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: T.209, H.239, L.242 Chain B: Y.271, K.272 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: R.392, P.432 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: G.206, T.207, P.236, H.239 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: G.278, L.279, R.325, Y.358 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: D.338, E.339, W.340 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: R.365, E.366, N.367, D.368 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: V.422, K.423, H.424, Q.425 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: R.411, K.416, D.418 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain B: H.17, W.21, P.225 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain A: Y.271, K.272 Chain B: T.209, H.239, L.242 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain B: H.117, R.224 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain B: Y.205, G.206, T.207, P.236, H.239 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: G.278, L.279, R.325, Y.358 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: E.366, N.367, D.368 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain B: D.42, E.43, R.335 Ligands: SO4.33 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: S.15, M.16, H.17 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain B: K.217, R.221 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: Q.176, K.217, R.221 Ligands: GOL.18 Ligand excluded by PLIP SO4.30: 1 residues within 4Å: Chain B: R.80 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain B: T.310, K.311, D.312 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain B: R.411, K.416 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain B: E.333, R.335, D.336 Ligands: SO4.26 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain C: H.17, W.21, P.225 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain C: G.278, L.279, R.325, Y.358 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain C: P.72, P.84, L.85, E.86 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain C: Q.176, R.221 Ligands: GOL.39 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain C: G.206, T.207, P.236, H.239 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain C: T.209, H.239, L.242 Chain D: Y.271, K.272 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain C: H.117, R.224 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain C: E.333, R.335, D.336 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain C: R.365, E.366, N.367 Ligand excluded by PLIP SO4.50: 4 residues within 4Å: Chain C: V.422, K.423, H.424, Q.425 Ligand excluded by PLIP SO4.51: 1 residues within 4Å: Chain C: R.80 Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Chain C: T.310, K.311 Ligand excluded by PLIP SO4.58: 6 residues within 4Å: Chain C: Y.271, K.272 Chain D: T.209, D.238, H.239, L.242 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain D: G.206, T.207, P.236, H.239 Ligand excluded by PLIP SO4.60: 4 residues within 4Å: Chain D: G.278, L.279, R.325, Y.358 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain D: D.42, E.43, R.335 Ligand excluded by PLIP SO4.62: 2 residues within 4Å: Chain D: H.117, R.224 Ligand excluded by PLIP SO4.63: 1 residues within 4Å: Chain D: R.80 Ligand excluded by PLIP SO4.64: 2 residues within 4Å: Chain D: T.310, K.311 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain D: R.392, G.431, P.432 Ligand excluded by PLIP SO4.66: 3 residues within 4Å: Chain D: Q.176, R.221 Ligands: GOL.56 Ligand excluded by PLIP SO4.67: 2 residues within 4Å: Chain D: K.217, R.221 Ligand excluded by PLIP

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.15: 8 residues within 4Å: Chain A: D.154, H.170, R.171, T.207, H.208, T.209, E.210, E.211 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.210, A:E.210 Hydrogen bonds: A:T.207, A:T.209, A:T.209, A:E.210, A:E.211 Water bridges: A:D.154, A:S.157, A:H.170 Salt bridges: A:H.170, A:R.171, A:H.208 CIT.34: 8 residues within 4Å: Chain B: R.129, H.170, R.171, T.207, H.208, T.209, E.210, E.211 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:E.210, B:E.210 Hydrogen bonds: B:R.129, B:D.169, B:T.209, B:T.209, B:E.210, B:E.211, B:E.211 Water bridges: B:S.157, B:S.157, B:H.170, B:R.171, B:R.171, B:R.171 Salt bridges: B:H.170, B:R.171, B:H.208 CIT.53: 10 residues within 4Å: Chain C: R.129, D.154, S.157, H.170, R.171, T.207, H.208, T.209, E.210, E.211 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:E.210, C:E.210 Hydrogen bonds: C:S.157, C:T.209, C:T.209, C:E.210, C:E.211 Water bridges: C:R.129, C:H.170, C:H.170 Salt bridges: C:H.170, C:R.171, C:H.208 CIT.68: 7 residues within 4Å: Chain D: H.170, R.171, T.207, H.208, T.209, E.210, E.211 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:H.208, D:T.209, D:E.210, D:E.211, D:E.211 Water bridges: D:R.129, D:H.170, D:E.211 Salt bridges: D:H.170, D:R.171, D:H.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lansky, S. et al., Structure-specificity relationships in Abp, a GH27 beta-L-arabinopyranosidase from Geobacillus stearothermophilus T6. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-12-03

Peptides

Abp, a GH27 beta-L-arabinopyranosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Abp, a GH27 beta-L-arabinopyranosidase

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