SMTL ID : 1dam.1

DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP, INORGANIC PHOSPHATE AND MAGNESIUM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 7 residues within 4Å: Chain A: T.16, K.37, D.54, E.115 Ligands: MG.2, PO4.3, ADP.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.16, A:D.54, A:E.115, H2O.4 MG.2: 4 residues within 4Å: Ligands: MG.1, PO4.3, ADP.4, DTB.5 No protein-ligand interaction detected (PLIP) MG.6: 7 residues within 4Å: Chain B: T.16, K.37, D.54, E.115 Ligands: MG.7, PO4.8, ADP.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.16, B:D.54, B:E.115, H2O.11 MG.7: 4 residues within 4Å: Ligands: MG.6, PO4.8, ADP.9, DTB.10 No protein-ligand interaction detected (PLIP)

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 11 residues within 4Å: Chain A: T.11, K.15, K.37, D.54, E.115, A.117, G.118 Ligands: MG.1, MG.2, ADP.4, DTB.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.54, A:D.54, A:G.118, A:G.118 Water bridges: A:E.12 Salt bridges: A:K.15, A:K.37 PO4.8: 11 residues within 4Å: Chain B: T.11, K.15, K.37, D.54, E.115, A.117, G.118 Ligands: MG.6, MG.7, ADP.9, DTB.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.11, B:D.54, B:D.54, B:G.118, B:G.118 Water bridges: B:E.12, B:T.16 Salt bridges: B:K.15, B:K.37

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

ADP.4: 20 residues within 4Å: Chain A: T.11, E.12, V.13, G.14, K.15, T.16, V.17, D.54, E.115, N.175, D.176, I.203, P.204, W.205, L.206, P.210, E.211 Ligands: MG.1, MG.2, PO4.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:E.12, A:V.13, A:G.14, A:K.15, A:T.16, A:T.16, A:V.17, A:N.175, A:N.175, A:L.206, A:E.211 Salt bridges: A:K.15 pi-Stacking: A:P.210, A:P.210 ADP.9: 20 residues within 4Å: Chain B: T.11, E.12, V.13, G.14, K.15, T.16, V.17, D.54, E.115, N.175, D.176, I.203, P.204, W.205, L.206, P.210, E.211 Ligands: MG.6, MG.7, PO4.8 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.11, B:E.12, B:V.13, B:G.14, B:K.15, B:T.16, B:V.17, B:N.175, B:N.175, B:L.206, B:E.211 Water bridges: B:T.16, B:T.16, B:E.211 Salt bridges: B:K.15 pi-Stacking: B:P.210, B:P.210

2 x DTB: 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID(Non-covalent)

DTB.5: 15 residues within 4Å: Chain A: T.11, S.41, T.80, S.81, A.117, G.118, T.122 Chain B: L.149, G.150, C.151, I.152, N.153, Y.187 Ligands: MG.2, PO4.3 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.117, A:T.122, B:L.149, B:I.152 Hydrogen bonds: A:T.11, A:T.11, A:S.41, B:G.150, B:I.152, B:N.153, B:Y.187 Water bridges: A:E.12, A:S.41, A:S.41, A:T.122 DTB.10: 15 residues within 4Å: Chain A: L.149, G.150, C.151, I.152, N.153, Y.187 Chain B: T.11, S.41, T.80, S.81, A.117, G.118, T.122 Ligands: MG.7, PO4.8 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.117, B:T.122, A:L.149, A:I.152 Hydrogen bonds: B:T.11, B:S.41, A:G.150, A:I.152, A:N.153 Water bridges: B:E.12, B:S.41, B:S.41, B:T.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kack, H. et al., Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis. Protein Sci. (1998)

Release Date

1999-01-13

Peptides

PROTEIN (DETHIOBIOTIN SYNTHETASE): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PROTEIN (DETHIOBIOTIN SYNTHETASE)

Related Entries With Identical Sequence