SMTL ID : 4nzf.2 (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

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: W.161, P.232, D.254, D.255 Ligands: ARB.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.254 GOL.2: 2 residues within 4Å: Chain A: K.217, R.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.217, A:R.221, A:R.221 GOL.3: 2 residues within 4Å: Chain A: H.117, R.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.224, A:R.224 Water bridges: A:H.117 GOL.4: 4 residues within 4Å: Chain A: P.72, P.84, L.85, E.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.84 Water bridges: A:E.86, A:E.86 GOL.18: 5 residues within 4Å: Chain B: W.161, P.232, D.254, D.255 Ligands: ARB.19 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.79, B:K.203, B:K.203 GOL.31: 4 residues within 4Å: Chain C: W.161, D.254, D.255 Ligands: ARB.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.255 GOL.41: 5 residues within 4Å: Chain D: W.161, P.232, D.254, D.255 Ligands: ARB.43 2 PLIP interactions: 2 interactions with chain D Water bridges: D:D.254, D:D.254 GOL.42: 6 residues within 4Å: Chain D: K.172, E.173, G.174, A.175, Q.176, A.177 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.172, D:G.174, D:A.175, D:Q.176, D:A.177

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

ARB.5: 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.195, A:K.195, A:S.231, A:R.251, A:R.251, A:D.255 Salt bridges: A:H.126 ARB.19: 13 residues within 4Å: Chain B: 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.18 8 PLIP interactions: 8 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, B:K.195 ARB.32: 14 residues within 4Å: Chain C: 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.31 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.195, C:K.195, C:D.198, C:S.231, C:S.231, C:R.251, C:R.251 Water bridges: C:K.195, C:R.251, C:D.255, C:D.286 Salt bridges: C:H.126 ARB.43: 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.41 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:W.32, D:K.195, D:D.198, D:S.231, D:S.231, D:S.231, D:R.251, D:R.251 Water bridges: D:K.195, D:D.255, D:D.255 Salt bridges: D:H.126, D:K.195

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

SO4.6: 3 residues within 4Å: Chain A: H.17, W.21, P.225 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: K.53, Y.54 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: G.278, L.279, R.325, Y.358 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: R.150 Chain C: P.84 Ligand excluded by PLIP SO4.10: 7 residues within 4Å: Chain A: K.172, E.173, G.174, A.175, Q.176, A.177 Ligands: SO4.11 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: Q.176, K.217, R.221 Ligands: SO4.10 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: G.206, T.207, P.236, H.239 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain A: T.209, H.239, L.242 Chain B: Y.271, K.272 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain A: T.310, K.311 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: E.333, R.335, D.336 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain A: V.422, K.423, H.424, Q.425 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain B: K.217, R.221 Ligand excluded by PLIP SO4.21: 6 residues within 4Å: Chain A: Y.271, K.272 Chain B: T.209, D.238, H.239, L.242 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: G.206, T.207, H.239 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain B: H.208, T.209, E.210, E.211 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: H.17, W.21, P.225 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain B: H.117, R.224 Ligand excluded by PLIP SO4.26: 7 residues within 4Å: Chain B: K.172, E.173, G.174, A.175, Q.176, A.177 Ligands: SO4.29 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain B: T.310, K.311 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain B: V.422, K.423, H.424, Q.425 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: Q.176, K.217, R.221 Ligands: SO4.26 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain B: G.278, L.279, R.325, Y.358 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain C: E.173, G.174, A.175, Q.176, A.177 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain C: G.278, L.279, R.325, Y.358 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain C: H.17, W.21, P.225 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain C: H.117, R.224 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain C: G.206, T.207, P.236, H.239 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain C: T.209, H.239, L.242 Chain D: Y.271, K.272 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain C: K.217, R.221 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain D: G.278, L.279, R.325 Ligand excluded by PLIP SO4.45: 2 residues within 4Å: Chain D: H.117, R.224 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain D: H.208, T.209, E.210, E.211 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain D: V.422, K.423, H.424, Q.425 Ligand excluded by PLIP SO4.48: 2 residues within 4Å: Chain B: P.84 Chain D: R.150 Ligand excluded by PLIP

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

CIT.17: 9 residues within 4Å: Chain A: D.154, D.169, H.170, R.171, T.207, H.208, T.209, E.210, E.211 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.210, A:E.210 Hydrogen bonds: A:D.169, A:T.207, A:T.209, A:E.210, A:E.211, A:E.211 Water bridges: A:R.129, A:S.157, A:V.168, A:H.170 Salt bridges: A:H.170, A:R.171, A:H.208 CIT.40: 10 residues within 4Å: Chain C: D.154, V.168, D.169, H.170, R.171, T.207, H.208, T.209, E.210, E.211 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:V.168, C:T.207, C:T.209, C:E.210, C:E.211, 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

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
E

B
F

C
G

D
H

Abp, a GH27 beta-L-arabinopyranosidase

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