SMTL ID : 5b7z.1

Crystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Ni2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 5 residues within 4Å: Chain A: R.137, R.173, Y.174, T.176, D.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.174 Water bridges: A:R.137 MPD.2: 8 residues within 4Å: Chain A: P.65, S.66, W.70, K.117, E.120, V.121, M.124 Ligands: 1PG.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.117, A:E.120 Hydrogen bonds: A:E.120 Water bridges: A:K.117, A:E.120, A:E.120 MPD.3: 4 residues within 4Å: Chain A: R.234, E.263, C.264, L.265 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.263 Hydrogen bonds: A:C.264 MPD.4: 4 residues within 4Å: Chain A: K.109, I.112, R.156 Ligands: 1PG.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.109 Hydrogen bonds: A:K.109 MPD.8: 4 residues within 4Å: Chain B: R.234, E.263, C.264, L.265 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.265 Hydrogen bonds: B:R.234, B:E.263, B:C.264 Water bridges: B:R.234

2 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 5 residues within 4Å: Chain A: E.169, D.202, H.228, R.234, E.263 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.169, A:D.202, A:H.228, A:E.263, H2O.2 NI.9: 4 residues within 4Å: Chain B: E.169, D.202, H.228, E.263 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.169, B:D.202, B:H.228, B:E.263, H2O.15

4 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.6: 5 residues within 4Å: Chain A: L.128, K.165, N.195, Y.225, R.258 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.165 Water bridges: A:Y.225, A:R.258 1PG.7: 7 residues within 4Å: Chain A: M.21, G.54, Q.56, F.279, K.283, I.286, I.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.283 1PG.10: 11 residues within 4Å: Chain A: E.113, V.116, L.160 Chain B: G.126, L.128, H.163, K.165, N.195, Y.225, R.258 Ligands: MPD.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.163, B:K.165 Water bridges: B:N.195, B:N.195, B:R.258 1PG.11: 10 residues within 4Å: Chain A: E.120 Chain B: L.189, N.193, S.194, N.195, V.197, E.222, K.223, Y.225 Ligands: MPD.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.223 Water bridges: B:S.194, B:S.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, S.M. et al., TM0416, a Hyperthermophilic Promiscuous Nonphosphorylated Sugar Isomerase, Catalyzes Various C5and C6Epimerization Reactions. Appl. Environ. Microbiol. (2017)

Release Date

2017-03-15

Peptides

Uncharacterized protein TM_0416: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uncharacterized protein TM_0416

Related Entries With Identical Sequence