SMTL ID : 3fsb.1 (1 other biounit)

Crystal structure of QdtC, the dTDP-3-amino-3,6-dideoxy-D-glucose N-acetyl transferase from Thermoanaerobacterium thermosaccharolyticum in complex with CoA and dTDP-3-amino-quinovose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

3 x COA: COENZYME A(Non-covalent)

COA.1: 19 residues within 4Å: Chain A: F.152, A.180, A.181, G.198, A.199, V.214, G.215 Chain C: T.158, N.159, D.160, P.161, P.163, L.186, P.187, T.204, K.205, N.216, P.217 Ligands: T3Q.2 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:D.160, C:P.161, C:T.204, C:K.205, C:N.216, A:A.181, A:A.199, A:A.199, A:G.215 Salt bridges: C:K.205, C:K.205 Water bridges: A:K.228 COA.3: 19 residues within 4Å: Chain A: T.158, N.159, D.160, P.161, P.163, L.186, P.187, T.204, K.205, N.216, P.217 Chain B: F.152, A.180, A.181, G.198, A.199, V.214, G.215 Ligands: T3Q.4 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:A.181, B:A.199, B:A.199, B:G.215, A:D.160, A:P.161, A:T.204, A:K.205, A:N.216 Water bridges: B:K.228 Salt bridges: A:K.205, A:K.205 COA.5: 19 residues within 4Å: Chain B: T.158, N.159, D.160, P.161, P.163, L.186, P.187, T.204, K.205, N.216, P.217 Chain C: F.152, A.180, A.181, G.198, A.199, V.214, G.215 Ligands: T3Q.6 12 PLIP interactions: 5 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:A.181, C:A.199, C:A.199, C:G.215, B:D.160, B:P.161, B:T.204, B:K.205, B:N.216 Water bridges: C:K.228 Salt bridges: B:K.205, B:K.205

3 x T3Q: [(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate(Non-covalent)

T3Q.2: 24 residues within 4Å: Chain A: R.80, G.98, H.99, K.114, G.116, T.117, H.134, S.135, W.150, F.152, F.243, R.245 Chain C: V.58, Y.86, R.104, Q.122, H.123, E.141, N.159, D.160, P.164, S.165, L.168 Ligands: COA.1 28 PLIP interactions: 16 interactions with chain A, 12 interactions with chain C Hydrophobic interactions: A:W.150, A:F.243, C:V.58, C:P.164 Hydrogen bonds: A:R.80, A:T.117, A:T.117, A:S.135, C:Y.86, C:Y.86, C:E.141, C:N.159, C:D.160 Water bridges: A:R.245, A:R.245, C:V.58, C:R.104, C:H.123 Salt bridges: A:K.114, A:K.114, A:H.134, A:H.134, A:H.134, A:R.245, A:R.245, C:R.104 pi-Cation interactions: A:R.80, C:R.104 T3Q.4: 24 residues within 4Å: Chain A: V.58, Y.86, R.104, Q.122, H.123, E.141, N.159, D.160, P.164, S.165, L.168 Chain B: R.80, G.98, H.99, K.114, G.116, T.117, H.134, S.135, W.150, F.152, F.243, R.245 Ligands: COA.3 28 PLIP interactions: 12 interactions with chain A, 16 interactions with chain B Hydrophobic interactions: A:V.58, A:P.164, B:W.150, B:F.243 Hydrogen bonds: A:Y.86, A:Y.86, A:E.141, A:N.159, A:D.160, B:R.80, B:T.117, B:T.117, B:S.135 Water bridges: A:V.58, A:R.104, A:H.123, B:R.245, B:R.245 Salt bridges: A:R.104, B:K.114, B:K.114, B:H.134, B:H.134, B:H.134, B:R.245, B:R.245 pi-Cation interactions: A:R.104, B:R.80 T3Q.6: 24 residues within 4Å: Chain B: V.58, Y.86, R.104, Q.122, H.123, E.141, N.159, D.160, P.164, S.165, L.168 Chain C: R.80, G.98, H.99, K.114, G.116, T.117, H.134, S.135, W.150, F.152, F.243, R.245 Ligands: COA.5 28 PLIP interactions: 12 interactions with chain B, 16 interactions with chain C Hydrophobic interactions: B:V.58, B:P.164, C:W.150, C:F.243 Hydrogen bonds: B:Y.86, B:Y.86, B:E.141, B:N.159, B:D.160, C:R.80, C:T.117, C:T.117, C:S.135 Water bridges: B:V.58, B:R.104, B:H.123, C:R.245, C:R.245 Salt bridges: B:R.104, C:K.114, C:K.114, C:H.134, C:H.134, C:H.134, C:R.245, C:R.245 pi-Cation interactions: B:R.104, C:R.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J. et al., Structural and Functional Studies of QdtC: an N-Acetyltransferase Required for the Biosynthesis of dTDP-3-Acetamido-3,6-Dideoxy-alpha-D-Glucose. Biochemistry (2009)

Release Date

2009-02-17

Peptides

QdtC: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

QdtC

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