SMTL ID : 1daf.1

DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID, ADP, AND CALCIUM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: D.54 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.54, H2O.6, H2O.6, H2O.6, H2O.6 CA.4: 2 residues within 4Å: Chain B: D.54 Ligands: ADP.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.54, H2O.12, H2O.12, H2O.12, H2O.12

2 x DSD: 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID(Non-covalent)

DSD.2: 15 residues within 4Å: Chain A: T.11, E.12, K.37, A.40, S.41, P.79, T.80, S.81, A.117, G.118 Chain B: G.150, C.151, I.152, N.153, Y.187 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.79 Hydrogen bonds: A:E.12, A:K.37, A:S.41, A:S.41, A:S.41, A:G.118, B:G.150, B:I.152, B:N.153, B:Y.187 Water bridges: A:N.52, A:T.122 DSD.5: 15 residues within 4Å: Chain A: G.150, C.151, I.152, N.153, Y.187 Chain B: T.11, E.12, K.37, A.40, S.41, P.79, T.80, S.81, A.117, G.118 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:G.150, A:I.152, A:N.153, B:T.11, B:E.12, B:K.37, B:S.41, B:S.41, B:S.41, B:G.118 Hydrophobic interactions: B:P.79 Water bridges: B:N.52, B:T.122

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

ADP.3: 17 residues within 4Å: Chain A: 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: CA.1 19 PLIP interactions: 19 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:T.16, A:V.17, A:E.115, A:N.175, A:P.204, A:L.206, A:E.211 Water bridges: A:T.11, A:E.12, A:K.15, A:T.16, A:D.54 Salt bridges: A:K.15 ADP.6: 17 residues within 4Å: Chain B: 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: CA.4 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:E.12, B:V.13, B:G.14, B:K.15, B:T.16, B:T.16, B:T.16, B:V.17, B:E.115, B:N.175, B:P.204, B:L.206, B:E.211 Water bridges: B:T.11, B:T.11, B:T.16, B:D.54, B:E.211 Salt bridges: B:K.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, W. et al., Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate. Biochemistry (1995)

Release Date

1996-06-20

Peptides

DETHIOBIOTIN SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DETHIOBIOTIN SYNTHETASE

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