SMTL ID : 2d2x.1

Crystal structure of 2-deoxy-scyllo-inosose synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x CO: COBALT (II) ION(Non-covalent)

CO.1: 4 residues within 4Å: Chain A: D.135, E.183, H.246, H.262 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.183, A:H.246, A:H.262, H2O.7, H2O.8 CO.2: 7 residues within 4Å: Chain A: D.42, G.102, G.103, G.104, L.105, T.106 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.42 CO.3: 4 residues within 4Å: Chain A: E.235, G.239, F.242, E.243 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.235, A:G.239, H2O.1, H2O.1 CO.6: 5 residues within 4Å: Chain B: D.135, E.183, H.246, H.262 Ligands: GOL.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.183, B:H.246, B:H.262, H2O.15

2 x SO3: SULFITE ION(Non-covalent)

SO3.4: 8 residues within 4Å: Chain A: E.243, Y.244, G.245, H.246, T.247, A.273, M.335, I.336 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.245, A:T.247, A:T.247, A:T.247, A:I.248, A:I.336, A:I.336 Water bridges: A:G.249 SO3.7: 8 residues within 4Å: Chain B: E.243, Y.244, G.245, H.246, T.247, A.273, M.335, I.336 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.245, B:T.247, B:T.247, B:T.247, B:I.248, B:I.336, B:I.336 Water bridges: B:G.249

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: G.103, G.104, T.129, L.131, A.132 Ligands: CO.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.104, A:L.105, A:T.129, A:A.132 GOL.8: 6 residues within 4Å: Chain B: G.103, G.104, T.129, L.131, A.132, Q.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.104, B:A.132 Water bridges: B:G.103 GOL.9: 5 residues within 4Å: Chain B: D.135, E.183, H.246, H.262 Ligands: CO.6 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nango, E. et al., Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+. Proteins (2008)

Release Date

2006-10-03

Peptides

2-deoxy-scyllo-inosose synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-deoxy-scyllo-inosose synthase

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