SMTL ID : 2olc.2 (1 other biounit)

Crystal structure of 5-methylthioribose kinase in complex with ADP-2Ho

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x HO: HOLMIUM ATOM(Non-covalent)

HO.1: 2 residues within 4Å: Chain A: D.250 Ligands: ADP.4 Ligand excluded by PLIP HO.2: 3 residues within 4Å: Chain A: D.250, E.252 Ligands: ADP.4 Ligand excluded by PLIP HO.5: 3 residues within 4Å: Chain B: D.250 Ligands: HO.6, ADP.7 Ligand excluded by PLIP HO.6: 4 residues within 4Å: Chain B: D.250, E.252 Ligands: HO.5, ADP.7 Ligand excluded by PLIP HO.8: 2 residues within 4Å: Chain C: D.250 Ligands: ADP.11 Ligand excluded by PLIP HO.9: 3 residues within 4Å: Chain C: D.250, E.252 Ligands: ADP.11 Ligand excluded by PLIP HO.12: 3 residues within 4Å: Chain D: D.250 Ligands: HO.13, ADP.14 Ligand excluded by PLIP HO.13: 4 residues within 4Å: Chain D: D.250, E.252 Ligands: HO.12, ADP.14 Ligand excluded by PLIP

2 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.3: 10 residues within 4Å: Chain A: K.377, E.380, D.386, E.389, L.390, L.393 Chain D: K.377, E.380, L.393, L.394 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:K.377, A:D.386, A:E.389, A:L.390, A:L.393, D:L.393, D:L.394 Hydrogen bonds: A:E.389, D:E.380 CPS.10: 10 residues within 4Å: Chain B: K.377, E.380, L.393, L.394 Chain C: K.377, E.380, D.386, E.389, L.390, L.393 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:L.393, B:L.394, C:K.377, C:D.386, C:E.389, C:L.390, C:L.393 Hydrogen bonds: B:E.380, C:E.389

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 18 residues within 4Å: Chain A: I.38, D.40, N.44, V.46, I.59, K.61, M.114, E.115, D.116, L.117, S.118, I.122, F.240, I.249, D.250, E.252 Ligands: HO.1, HO.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.40, A:G.41, A:N.44, A:E.115, A:L.117 Water bridges: A:D.40 Salt bridges: A:K.61, A:K.61 pi-Stacking: A:F.240 ADP.7: 18 residues within 4Å: Chain B: I.38, D.40, G.41, N.44, V.46, I.59, K.61, M.114, E.115, D.116, L.117, S.118, I.122, F.240, D.250, E.252 Ligands: HO.5, HO.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.40, B:N.44, B:E.115, B:D.116, B:L.117 Salt bridges: B:K.61, B:K.61 pi-Stacking: B:F.240 ADP.11: 18 residues within 4Å: Chain C: I.38, D.40, N.44, V.46, I.59, K.61, M.114, E.115, D.116, L.117, S.118, I.122, F.240, I.249, D.250, E.252 Ligands: HO.8, HO.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.40, C:G.41, C:N.44, C:E.115, C:L.117 Water bridges: C:D.40 Salt bridges: C:K.61, C:K.61 pi-Stacking: C:F.240 ADP.14: 18 residues within 4Å: Chain D: I.38, D.40, G.41, N.44, V.46, I.59, K.61, M.114, E.115, D.116, L.117, S.118, I.122, F.240, D.250, E.252 Ligands: HO.12, HO.13 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:D.40, D:N.44, D:E.115, D:D.116, D:L.117 Salt bridges: D:K.61, D:K.61 pi-Stacking: D:F.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ku, S.Y. et al., ADP-2Ho as a phasing tool for nucleotide-containing proteins. Acta Crystallogr.,Sect.D (2007)

Release Date

2007-05-22

Peptides

Methylthioribose kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Methylthioribose kinase

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