SMTL ID : 1dak.1

DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: K.148, L.149, R.183, H.184, Y.187 3 PLIP interactions: 3 interactions with chain A Water bridges: A:L.149, A:R.183, A:H.184 PO4.6: 5 residues within 4Å: Chain B: K.148, L.149, R.183, H.184, Y.187 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.149, B:R.183

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: T.16, K.37, D.54, E.115 Ligands: MG.3, DPU.4, ADP.5 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.3: 4 residues within 4Å: Chain A: E.12 Ligands: MG.2, DPU.4, ADP.5 No protein-ligand interaction detected (PLIP) MG.7: 7 residues within 4Å: Chain B: T.16, K.37, D.54, E.115 Ligands: MG.8, DPU.9, ADP.10 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 MG.8: 4 residues within 4Å: Chain B: E.12 Ligands: MG.7, DPU.9, ADP.10 No protein-ligand interaction detected (PLIP)

2 x DPU: MIXED CARBAMIC PHOSPHORIC ACID ANHYDRIDE OF 7,8-DIAMINONONANIC ACID(Non-covalent)

DPU.4: 22 residues within 4Å: Chain A: T.11, K.15, K.37, A.40, S.41, D.54, P.79, T.80, S.81, E.115, A.117, G.118, T.122 Chain B: L.149, G.150, C.151, I.152, N.153, Y.187 Ligands: MG.2, MG.3, ADP.5 21 PLIP interactions: 7 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:L.149, A:P.79 Hydrogen bonds: B:G.150, B:I.152, B:N.153, B:Y.187, B:Y.187, A:T.11, A:T.11, A:K.37, A:S.41, A:S.41, A:G.118, A:G.118 Water bridges: B:N.153, A:E.12, A:N.52, A:D.54, A:D.54 Salt bridges: A:K.15, A:K.37 DPU.9: 22 residues within 4Å: Chain A: L.149, G.150, C.151, I.152, N.153, Y.187 Chain B: T.11, K.15, K.37, A.40, S.41, D.54, P.79, T.80, S.81, E.115, A.117, G.118, T.122 Ligands: MG.7, MG.8, ADP.10 22 PLIP interactions: 16 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:P.79, A:L.149 Hydrogen bonds: B:T.11, B:T.11, B:K.37, B:S.41, B:S.41, B:E.115, B:G.118, B:G.118, A:G.150, A:I.152, A:N.153, A:Y.187 Water bridges: B:E.12, B:T.16, B:N.52, B:D.54, B:D.54, A:N.153 Salt bridges: B:K.15, B:K.37

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

ADP.5: 20 residues within 4Å: Chain A: D.10, T.11, E.12, V.13, G.14, K.15, T.16, V.17, E.115, N.175, D.176, I.203, P.204, W.205, L.206, P.210, E.211 Ligands: MG.2, MG.3, DPU.4 14 PLIP interactions: 14 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:N.175, A:P.204, A:L.206, A:E.211 Water bridges: A:E.12 Salt bridges: A:K.15 ADP.10: 20 residues within 4Å: Chain B: D.10, T.11, E.12, V.13, G.14, K.15, T.16, V.17, E.115, N.175, D.176, I.203, P.204, W.205, L.206, P.210, E.211 Ligands: MG.7, MG.8, DPU.9 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.11, B:E.12, B:E.12, B:V.13, B:G.14, B:K.15, B:T.16, B:V.17, B:N.175, B:P.204, B:L.206, B:E.211 Water bridges: B:T.16, B:T.16, B:E.211, B:E.211 Salt bridges: B:K.15

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

1999-04-06

Peptides

DETHIOBIOTIN SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DETHIOBIOTIN SYNTHETASE

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