SMTL ID : 3a9s.1

X-ray Structure of Bacillus pallidus D-Arabinose Isomerase Complex with Glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: M.190, Q.307, E.342, D.366, S.398 Chain B: R.23, W.95, V.124 Ligands: MN.2 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.307, A:E.342, A:D.366, A:S.398, B:R.23, B:R.23 Water bridges: A:N.531 GOL.4: 7 residues within 4Å: Chain A: N.49, V.50, F.51, K.169, L.357, T.358, N.359 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.51, A:F.51, A:K.169, A:L.357 GOL.5: 8 residues within 4Å: Chain B: M.190, Q.307, E.342, D.366, S.398 Chain C: R.23, W.95 Ligands: MN.6 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:R.23, C:R.23, B:Q.307, B:E.342, B:D.366, B:S.398 Water bridges: B:N.531 GOL.8: 7 residues within 4Å: Chain B: N.49, V.50, F.51, K.169, L.357, T.358, N.359 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.51, B:F.51, B:K.169, B:L.357 Water bridges: B:N.49, B:K.169 GOL.10: 9 residues within 4Å: Chain A: R.23, W.95, V.124 Chain C: M.190, Q.307, E.342, D.366, S.398 Ligands: MN.9 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.307, C:E.342, C:D.366, C:S.398, A:R.23, A:R.23 Water bridges: C:N.531 GOL.12: 7 residues within 4Å: Chain C: N.49, V.50, F.51, K.169, L.357, T.358, N.359 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:F.51, C:F.51, C:K.169, C:L.357 Water bridges: C:N.49, C:K.169 GOL.13: 9 residues within 4Å: Chain D: M.190, Q.307, E.342, D.366, S.398 Chain E: R.23, W.95, V.124 Ligands: MN.14 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:Q.307, D:E.342, D:D.366, D:S.398, E:R.23, E:R.23 Water bridges: D:N.531 GOL.16: 7 residues within 4Å: Chain D: N.49, V.50, F.51, K.169, L.357, T.358, N.359 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:F.51, D:F.51, D:K.169, D:L.357 GOL.17: 8 residues within 4Å: Chain E: M.190, Q.307, E.342, D.366, S.398 Chain F: R.23, W.95 Ligands: MN.18 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:Q.307, E:E.342, E:D.366, E:S.398, F:R.23, F:R.23 Water bridges: E:N.531 GOL.20: 7 residues within 4Å: Chain E: N.49, V.50, F.51, K.169, L.357, T.358, N.359 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:F.51, E:F.51, E:K.169, E:L.357 Water bridges: E:N.49, E:K.169 GOL.22: 9 residues within 4Å: Chain D: R.23, W.95, V.124 Chain F: M.190, Q.307, E.342, D.366, S.398 Ligands: MN.21 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:Q.307, F:E.342, F:D.366, F:S.398, D:R.23, D:R.23 Water bridges: F:N.531 GOL.24: 7 residues within 4Å: Chain F: N.49, V.50, F.51, K.169, L.357, T.358, N.359 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:F.51, F:F.51, F:K.169, F:L.357 Water bridges: F:N.49, F:K.169

12 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: E.342, D.366, N.397, S.398, H.532 Ligands: GOL.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.342, A:D.366, A:H.532, H2O.2 MN.3: 1 residues within 4Å: Chain A: D.453 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.453, H2O.5, H2O.5, H2O.5, H2O.6, H2O.6 MN.6: 5 residues within 4Å: Chain B: E.342, D.366, S.398, H.532 Ligands: GOL.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.342, B:D.366, B:H.532, H2O.23 MN.7: 1 residues within 4Å: Chain B: D.453 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.453, H2O.27, H2O.27, H2O.27, H2O.27, H2O.27 MN.9: 6 residues within 4Å: Chain C: E.342, D.366, N.397, S.398, H.532 Ligands: GOL.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.342, C:D.366, C:H.532, H2O.43 MN.11: 1 residues within 4Å: Chain C: D.453 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.453, H2O.47, H2O.47, H2O.47, H2O.47, H2O.47 MN.14: 6 residues within 4Å: Chain D: E.342, D.366, N.397, S.398, H.532 Ligands: GOL.13 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.342, D:D.366, D:H.532, H2O.62 MN.15: 1 residues within 4Å: Chain D: D.453 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.453, H2O.66, H2O.66, H2O.66, H2O.66, H2O.66 MN.18: 5 residues within 4Å: Chain E: E.342, D.366, S.398, H.532 Ligands: GOL.17 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.342, E:D.366, E:H.532, H2O.84 MN.19: 1 residues within 4Å: Chain E: D.453 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:D.453, H2O.87, H2O.87, H2O.87, H2O.87, H2O.87 MN.21: 6 residues within 4Å: Chain F: E.342, D.366, N.397, S.398, H.532 Ligands: GOL.22 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.342, F:D.366, F:H.532, H2O.104 MN.23: 1 residues within 4Å: Chain F: D.453 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:D.453, H2O.108, H2O.108, H2O.108, H2O.108, H2O.108

Links

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Citation

Takeda, K. et al., X-ray structures of Bacillus pallidusd-arabinose isomerase and its complex with l-fucitol. Biochim.Biophys.Acta (2010)

Release Date

2010-04-07

Peptides

D-arabinose isomerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

D-arabinose isomerase

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