SMTL ID : 2gru.1

Crystal structure of 2-deoxy-scyllo-inosose synthase complexed with carbaglucose-6-phosphate, NAD+ and Co2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

CO.1: 5 residues within 4Å: Chain A: D.135, E.183, H.246, H.262 Ligands: EXO.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.183, A:H.246, A:H.262, H2O.4 CO.7: 5 residues within 4Å: Chain B: D.135, E.183, H.246, H.262 Ligands: CAK.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.183, B:H.246, B:H.262, H2O.10

2 x SO3: SULFITE ION(Non-covalent)

SO3.2: 9 residues within 4Å: Chain A: E.243, Y.244, G.245, H.246, T.247, I.248, A.273, M.335, I.336 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.245, A:T.247, A:T.247, A:I.248, A:I.336, A:I.336 Water bridges: A:G.249 SO3.8: 9 residues within 4Å: Chain B: E.243, Y.244, G.245, H.246, T.247, I.248, A.273, M.335, I.336 7 PLIP interactions: 7 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

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

PO4.3: 5 residues within 4Å: Chain A: K.141, N.151, K.322 Chain B: R.119 Ligands: EXO.5 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.119, A:K.141, A:K.322 Hydrogen bonds: A:N.151

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.4: 22 residues within 4Å: Chain A: D.42, G.44, V.45, P.46, I.49, E.72, K.75, G.103, G.104, L.105, N.108, T.128, T.129, L.131, A.132, S.136, S.139, K.141, N.151, P.173, Q.176 Ligands: EXO.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:D.42, A:E.72, A:K.75, A:G.103, A:G.104, A:L.105, A:N.108, A:T.128, A:T.129, A:A.132, A:S.139, A:K.141, A:N.151, A:Q.176 Water bridges: A:G.103, A:T.106, A:Q.142 NAD.9: 21 residues within 4Å: Chain A: R.119 Chain B: D.42, G.44, V.45, P.46, I.49, E.72, K.75, G.103, G.104, L.105, N.108, T.128, T.129, L.131, S.136, K.150, N.151, P.173, Q.176 Ligands: CAK.10 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.42, B:E.72, B:G.103, B:G.104, B:L.105, B:N.108, B:T.128, B:T.128, B:A.132, B:K.150, B:K.150, B:N.151, B:N.151, B:Q.176, B:Q.176, A:R.119 Water bridges: B:T.106

1 x EXO: (1R,2S,3S,4R)-5-METHYLENECYCLOHEXANE-1,2,3,4-TETRAOL(Non-covalent)

EXO.5: 12 residues within 4Å: Chain A: D.135, E.183, K.186, K.225, E.235, F.242, E.243, H.246, H.262 Ligands: CO.1, PO4.3, NAD.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.135, A:K.186, A:K.225, A:E.235 Water bridges: A:D.135

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 6 residues within 4Å: Chain A: S.48, I.49, Y.52, R.167, I.168, E.171 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.49, A:Y.52, A:R.167 MPD.11: 5 residues within 4Å: Chain B: N.278, N.281, L.282, M.283, P.284 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.278

1 x CAK: [(1R,2R,3S,4S,5R)-2,3,4,5-TETRAHYDROXYCYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE(Non-covalent)

CAK.10: 16 residues within 4Å: Chain A: R.119 Chain B: D.135, S.139, K.141, N.151, E.183, K.186, K.225, E.235, F.242, E.243, H.246, H.250, H.262 Ligands: CO.7, NAD.9 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Salt bridges: A:R.119, B:K.141 Hydrogen bonds: B:D.135, B:S.139, B:N.151, B:K.186, B:K.225, B:K.225

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

2007-05-08

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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