SMTL ID : 7cyy.1

Crystal structure of Arabinose isomerase from hybrid AI8 with Adonitol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 7 residues within 4Å: Chain A: W.39, S.43, F.45, F.49, A.158, V.161, R.162 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.39, A:F.45, A:A.158, A:V.161, A:R.162 MPD.13: 7 residues within 4Å: Chain E: W.39, N.40, V.44, F.45, F.47, F.49, V.161 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:V.44, E:F.45, E:F.49, E:F.49, E:V.161 Hydrogen bonds: E:V.44, E:F.45

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

MN.2: 3 residues within 4Å: Chain A: D.195, G.398 Chain D: G.398 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: A:G.398, D:G.398, H2O.1, H2O.6, H2O.6 MN.3: 5 residues within 4Å: Chain A: E.307, E.332, H.349, H.448 Ligands: RB0.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.307, A:E.332, A:H.349, A:H.448 MN.5: 5 residues within 4Å: Chain B: E.307, E.332, H.349, H.448 Ligands: RB0.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.307, B:E.332, B:H.349, B:H.448 MN.6: 4 residues within 4Å: Chain B: D.195, G.398 Chain E: D.195, G.398 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:G.398, H2O.3, H2O.4, H2O.7, H2O.8 MN.9: 5 residues within 4Å: Chain C: E.307, E.332, H.349, H.448 Ligands: RB0.8 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.307, C:E.307, C:E.332, C:H.349, C:H.448 MN.10: 5 residues within 4Å: Chain C: D.195, D.396, G.398 Chain F: D.195, G.398 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: C:G.398, F:G.398, H2O.8, H2O.9 MN.12: 5 residues within 4Å: Chain D: E.307, E.332, H.349, H.448 Ligands: RB0.11 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.307, D:E.307, D:E.332, D:H.349, D:H.448 MN.14: 5 residues within 4Å: Chain E: E.307, E.332, H.349, H.448 Ligands: RB0.15 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.307, E:E.307, E:E.332, E:H.349, E:H.448 MN.17: 5 residues within 4Å: Chain F: E.307, E.332, H.349, H.448 Ligands: RB0.16 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.307, F:E.332, F:H.349, F:H.448

6 x RB0: D-ribitol(Non-covalent)(Post Translational Modification)

RB0.4: 15 residues within 4Å: Chain A: Q.17, L.19, Y.20, F.84, Q.126, H.129 Chain B: E.307, E.332, Y.334, H.349, M.350, I.371, H.447, H.448 Ligands: MN.5 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.17, A:Q.126, A:H.129, B:E.307 RB0.7: 15 residues within 4Å: Chain A: F.280, E.307, E.332, Y.334, M.350, I.371, H.447, H.448 Chain C: L.19, Y.20, F.84, N.123, Q.126, H.129 Ligands: MN.3 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.126, C:Q.126, A:E.307, A:Y.334 RB0.8: 15 residues within 4Å: Chain B: Q.17, L.19, Y.20, F.84, Q.126, H.129 Chain C: M.186, E.307, E.332, Y.334, H.349, M.350, H.447, H.448 Ligands: MN.9 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.17, B:Q.126, C:Y.334, C:H.447 RB0.11: 16 residues within 4Å: Chain D: M.186, F.280, E.307, E.332, Y.334, H.349, M.350, I.371, H.447, H.448 Chain E: Q.17, Y.20, F.84, Q.126, H.129 Ligands: MN.12 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:E.332, D:Y.334, D:Y.334, E:Q.17, E:Q.17, E:Q.126 RB0.15: 15 residues within 4Å: Chain E: M.186, F.280, E.307, E.332, Y.334, H.349, M.350, I.371, H.447, H.448 Chain F: L.19, Y.20, F.84, H.129 Ligands: MN.14 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.20, F:H.129 RB0.16: 13 residues within 4Å: Chain D: Q.17, Y.20, F.84, N.123, Q.126, H.129 Chain F: E.307, E.332, Y.334, H.349, H.447, H.448 Ligands: MN.17 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:Q.17, D:Q.126, D:Q.126, F:H.447

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoang, N.K.Q. et al., Crystal structure of Arabinose isomerase from hyper thermophilic hybrid AI8 with Adonitol. To Be Published

Release Date

2021-09-08

Peptides

L-arabinose isomerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
C

F
F

L-arabinose isomerase

Related Entries With Identical Sequence