SMTL ID : 1a82.1

DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX WITH SUBSTRATES ATP AND DIAMINOPELARGONIC ACID

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.16, K.37, D.54, E.115 Ligands: ATP.3 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.4: 5 residues within 4Å: Chain B: T.16, K.37, D.54, E.115 Ligands: ATP.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.16, B:D.54, B:E.115, H2O.12

2 x DNN: 7,8-DIAMINO-NONANOIC ACID(Non-covalent)

DNN.2: 15 residues within 4Å: Chain A: T.11, E.12, S.41, P.79, T.80, S.81, G.118, T.122 Chain B: L.149, G.150, C.151, I.152, N.153, Y.187 Ligands: ATP.3 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:P.79, B:L.149 Hydrogen bonds: A:T.11, A:T.11, B:G.150, B:I.152, B:N.153, B:Y.187, B:Y.187 Water bridges: A:K.37, A:S.41, A:S.41 DNN.5: 15 residues within 4Å: Chain A: L.149, G.150, C.151, I.152, N.153, Y.187 Chain B: T.11, E.12, S.41, P.79, T.80, S.81, G.118, T.122 Ligands: ATP.6 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:P.79, A:L.149 Hydrogen bonds: B:T.11, A:G.150, A:I.152, A:N.153, A:Y.187 Water bridges: B:K.37, B:S.41, B:S.41

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 21 residues within 4Å: Chain A: T.11, E.12, V.13, G.14, K.15, T.16, V.17, K.37, D.54, E.115, G.118, N.175, D.176, I.203, P.204, W.205, L.206, P.210, E.211 Ligands: MG.1, DNN.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:E.12, A:E.12, A:V.13, A:G.14, A:K.15, A:T.16, A:T.16, A:V.17, A:G.118, A:N.175, A:P.204, A:L.206, A:E.211 Water bridges: A:T.16, A:D.54 Salt bridges: A:K.15, A:K.15, A:K.37 ATP.6: 21 residues within 4Å: Chain B: T.11, E.12, V.13, G.14, K.15, T.16, V.17, K.37, D.54, E.115, G.118, N.175, D.176, I.203, P.204, W.205, L.206, P.210, E.211 Ligands: MG.4, DNN.5 20 PLIP interactions: 20 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:G.118, B:N.175, B:P.204, B:L.206, B:E.211 Water bridges: B:T.16, B:T.16, B:D.54, B:E.211, B:E.211 Salt bridges: B:K.15, B:K.15, B:K.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kack, H. et al., Snapshot of a phosphorylated substrate intermediate by kinetic crystallography. Proc.Natl.Acad.Sci.USA (1998)

Release Date

1999-05-11

Peptides

DETHIOBIOTIN SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DETHIOBIOTIN SYNTHETASE

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