SMTL ID : 3a9r.1

X-ray Structures of Bacillus pallidus D-Arabinose IsomeraseComplex with (4R)-2-METHYLPENTANE-2,4-DIOL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-hexamer

Ligands

6 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.1: 13 residues within 4Å: Chain A: M.190, Q.307, E.342, D.366, S.398, Y.444, F.445, W.503 Chain B: R.23, W.95, P.121, V.124 Ligands: MN.2 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.95, B:W.95, B:P.121, B:V.124, A:Y.444, A:Y.444, A:F.445, A:W.503 Hydrogen bonds: B:R.23, B:R.23, A:E.342 MRD.4: 13 residues within 4Å: Chain B: M.190, Q.307, E.342, D.366, S.398, Y.444, F.445, W.503 Chain C: R.23, W.95, P.121, V.124 Ligands: MN.5 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:W.95, C:W.95, C:P.121, C:V.124, B:Y.444, B:Y.444, B:F.445, B:W.503 Hydrogen bonds: C:R.23, C:R.23, B:Q.307, B:E.342 MRD.7: 10 residues within 4Å: Chain A: R.23, W.95, V.124 Chain C: M.190, Q.307, E.342, S.398, Y.444, F.445 Ligands: MN.8 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.95, A:V.124, C:F.445 Hydrogen bonds: A:R.23, A:R.23, C:Q.307, C:E.342 MRD.10: 13 residues within 4Å: Chain D: M.190, Q.307, E.342, D.366, S.398, Y.444, F.445, W.503 Chain E: R.23, W.95, P.121, V.124 Ligands: MN.11 11 PLIP interactions: 6 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:W.95, E:W.95, E:P.121, E:V.124, D:Y.444, D:Y.444, D:F.445, D:W.503 Hydrogen bonds: E:R.23, E:R.23, D:E.342 MRD.13: 13 residues within 4Å: Chain E: M.190, Q.307, E.342, D.366, S.398, Y.444, F.445, W.503 Chain F: R.23, W.95, P.121, V.124 Ligands: MN.14 12 PLIP interactions: 6 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:Y.444, E:Y.444, E:F.445, E:W.503, F:W.95, F:W.95, F:P.121, F:V.124 Hydrogen bonds: E:Q.307, E:E.342, F:R.23, F:R.23 MRD.16: 10 residues within 4Å: Chain D: R.23, W.95, V.124 Chain F: M.190, Q.307, E.342, S.398, Y.444, F.445 Ligands: MN.17 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:W.95, D:V.124, F:F.445 Hydrogen bonds: D:R.23, D:R.23, F:Q.307, F:E.342

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: MRD.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.342, A:D.366, A:D.366, A:H.532 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.3, H2O.3, H2O.3, H2O.3, H2O.3 MN.5: 6 residues within 4Å: Chain B: E.342, D.366, N.397, S.398, H.532 Ligands: MRD.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.342, B:D.366, B:D.366, B:H.532 MN.6: 2 residues within 4Å: Chain B: D.453, D.496 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.453, H2O.19, H2O.19, H2O.19, H2O.19, H2O.19 MN.8: 6 residues within 4Å: Chain C: E.342, D.366, N.397, S.398, H.532 Ligands: MRD.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.342, C:D.366, C:H.532 MN.9: 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.35, H2O.35, H2O.35, H2O.35, H2O.36 MN.11: 6 residues within 4Å: Chain D: E.342, D.366, N.397, S.398, H.532 Ligands: MRD.10 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.342, D:D.366, D:D.366, D:H.532 MN.12: 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.49, H2O.49, H2O.49, H2O.49, H2O.49 MN.14: 6 residues within 4Å: Chain E: E.342, D.366, N.397, S.398, H.532 Ligands: MRD.13 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.342, E:D.366, E:D.366, E:H.532 MN.15: 2 residues within 4Å: Chain E: D.453, D.496 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:D.453, H2O.66, H2O.66, H2O.66, H2O.66, H2O.66 MN.17: 6 residues within 4Å: Chain F: E.342, D.366, N.397, S.398, H.532 Ligands: MRD.16 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.342, F:D.366, F:H.532 MN.18: 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.82, H2O.82, H2O.82, H2O.82, H2O.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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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