SMTL ID : 7cx7.1

Crystal structure of Arabinose isomerase from hybrid AI8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-hexamer

Ligands

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

MPD.1: 8 residues within 4Å: Chain A: W.39, V.44, F.45, F.47, F.49, A.158, V.161, R.162 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.39, A:F.45, A:F.49, A:F.49, A:F.49, A:A.158, A:V.161, A:V.161 Hydrogen bonds: A:W.39 MPD.2: 7 residues within 4Å: Chain A: R.98, A.171, R.175, R.202, F.203, M.466, A.467 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.467 Hydrogen bonds: A:A.171, A:R.175, A:F.203 MPD.5: 8 residues within 4Å: Chain B: R.98, A.171, R.175, A.201, R.202, F.203, M.466, A.467 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.171 Hydrogen bonds: B:R.98 MPD.7: 6 residues within 4Å: Chain C: W.39, F.45, F.49, A.158, V.161, R.162 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.39, C:F.45, C:F.49, C:F.49 Hydrogen bonds: C:W.39, C:W.39, C:R.162 MPD.8: 9 residues within 4Å: Chain C: R.98, P.100, A.171, R.175, R.202, F.203, F.463, M.466, A.467 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.171, C:R.175, C:F.463, C:M.466 Hydrogen bonds: C:R.175, C:F.203 MPD.11: 6 residues within 4Å: Chain D: W.39, D.42, F.45, F.49, A.158, R.162 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.39, D:D.42, D:F.45, D:F.49 MPD.12: 8 residues within 4Å: Chain D: R.98, A.171, R.175, R.202, F.203, G.204, M.466, A.467 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.171, D:M.466, D:A.467 Hydrogen bonds: D:A.171, D:F.203 MPD.17: 7 residues within 4Å: Chain F: W.39, P.46, F.47, F.49, A.158, V.161, R.162 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:F.49, F:F.49, F:A.158, F:V.161, F:R.162 Hydrogen bonds: F:W.39 MPD.18: 8 residues within 4Å: Chain F: A.171, R.175, A.201, R.202, F.203, G.204, M.466, A.467 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:R.175 Hydrogen bonds: F:A.171, F:R.175, F:R.202

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

MN.3: 4 residues within 4Å: Chain A: E.307, E.332, H.349, H.448 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.307, A:E.307, A:E.332, A:H.349, A:H.448 MN.4: 4 residues within 4Å: Chain A: D.195, G.398 Chain B: D.195, G.398 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:G.398, B:G.398, H2O.2 MN.6: 4 residues within 4Å: Chain B: E.307, E.332, H.349, H.448 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.307, B:E.332, B:H.349, B:H.448, H2O.6 MN.9: 3 residues within 4Å: Chain C: D.195, G.398 Chain F: 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.14 MN.10: 5 residues within 4Å: Chain C: E.307, E.332, H.349, H.447, H.448 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.307, C:E.332, C:H.349, C:H.448, H2O.9 MN.14: 3 residues within 4Å: Chain D: D.195, G.398 Chain E: G.398 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: E:G.398, D:G.398, H2O.9, H2O.12, H2O.12 MN.15: 4 residues within 4Å: Chain D: E.307, E.332, H.349, H.448 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.307, D:E.332, D:H.349, D:H.448, H2O.11 MN.16: 5 residues within 4Å: Chain E: E.307, E.332, H.349, H.447, H.448 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.307, E:E.332, E:E.332, E:H.349, E:H.448 MN.19: 4 residues within 4Å: Chain F: E.307, E.332, H.349, H.448 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.307, F:E.332, F:H.349, F:H.448

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 6 residues within 4Å: Chain D: Q.461, C.471, V.472, V.473, F.483, E.486 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.461, D:V.473, D:E.486, B:N.485 Water bridges: D:N.490

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoang, N.K.Q. et al., Crystal structure of Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) wt. To Be Published

Release Date

2021-09-01

Peptides

L-arabinose isomerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
C

E
D

F
F

L-arabinose isomerase

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