SMTL ID : 4ecm.1

2.3 Angstrom Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase from Bacillus anthracis in Complex with Thymidine-5-diphospho-alpha-D-glucose and Pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x DAU: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE(Non-covalent)

DAU.1: 28 residues within 4Å: Chain A: L.30, A.31, G.32, G.33, R.37, K.47, H.48, Q.104, A.107, G.108, G.109, I.110, A.113, L.130, G.131, D.132, N.133, F.166, G.167, E.181, K.182, V.192, G.194, R.214, E.216, T.220, W.241 Ligands: POP.2 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.32, A:G.33, A:K.47, A:Q.104, A:Q.104, A:G.109, A:G.131, A:D.132, A:D.132, A:N.133, A:N.133, A:G.167, A:E.181, A:V.192, A:R.214 Water bridges: A:R.37, A:R.37, A:R.37, A:Y.196, A:R.214, A:I.219 Salt bridges: A:R.37, A:R.37, A:K.182, A:K.182 DAU.3: 28 residues within 4Å: Chain B: L.30, A.31, G.32, G.33, R.37, K.47, H.48, Q.104, A.107, G.108, G.109, I.110, A.113, L.130, G.131, D.132, N.133, F.166, G.167, E.181, K.182, V.192, G.194, R.214, E.216, T.220, W.241 Ligands: POP.4 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:G.32, B:G.33, B:K.47, B:Q.104, B:Q.104, B:G.109, B:G.131, B:D.132, B:D.132, B:N.133, B:N.133, B:G.167, B:E.181, B:V.192, B:R.214 Water bridges: B:R.37, B:R.37, B:R.37, B:Y.196, B:R.214, B:I.219 Salt bridges: B:R.37, B:R.37, B:K.182, B:K.182 DAU.5: 28 residues within 4Å: Chain C: L.30, A.31, G.32, G.33, R.37, K.47, H.48, Q.104, A.107, G.108, G.109, I.110, A.113, L.130, G.131, D.132, N.133, F.166, G.167, E.181, K.182, V.192, G.194, R.214, E.216, T.220, W.241 Ligands: POP.6 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:G.32, C:G.33, C:K.47, C:Q.104, C:Q.104, C:G.109, C:G.131, C:D.132, C:D.132, C:N.133, C:N.133, C:G.167, C:E.181, C:V.192, C:R.214, C:T.220 Water bridges: C:R.37, C:R.37, C:R.37, C:E.218, C:E.218 Salt bridges: C:R.37, C:R.37, C:K.182, C:K.182 DAU.7: 28 residues within 4Å: Chain D: L.30, A.31, G.32, G.33, R.37, K.47, H.48, Q.104, A.107, G.108, G.109, I.110, A.113, L.130, G.131, D.132, N.133, F.166, G.167, E.181, K.182, V.192, G.194, R.214, E.216, T.220, W.241 Ligands: POP.8 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:G.32, D:G.33, D:K.47, D:Q.104, D:Q.104, D:G.109, D:G.131, D:D.132, D:D.132, D:N.133, D:N.133, D:G.167, D:E.181, D:V.192, D:R.214, D:T.220 Water bridges: D:R.37, D:R.37, D:R.37, D:E.218, D:E.218 Salt bridges: D:R.37, D:R.37, D:K.182, D:K.182

4 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 8 residues within 4Å: Chain A: G.32, G.33, T.34, G.35, S.36, R.37, K.47 Ligands: DAU.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.34, A:G.35, A:S.36, A:S.36, A:R.37 Water bridges: A:K.47, A:K.47 Salt bridges: A:R.37, A:R.37, A:K.47, A:K.47 POP.4: 8 residues within 4Å: Chain B: G.32, G.33, T.34, G.35, S.36, R.37, K.47 Ligands: DAU.3 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.34, B:G.35, B:S.36, B:S.36, B:R.37 Water bridges: B:K.47, B:K.47 Salt bridges: B:R.37, B:R.37, B:K.47, B:K.47 POP.6: 8 residues within 4Å: Chain C: G.32, G.33, T.34, G.35, S.36, R.37, K.47 Ligands: DAU.5 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.34, C:T.34, C:G.35, C:S.36, C:S.36, C:R.37 Water bridges: C:K.47, C:K.47 Salt bridges: C:R.37, C:R.37, C:K.47, C:K.47 POP.8: 8 residues within 4Å: Chain D: G.32, G.33, T.34, G.35, S.36, R.37, K.47 Ligands: DAU.7 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:T.34, D:T.34, D:G.35, D:S.36, D:S.36, D:R.37 Water bridges: D:K.47, D:K.47 Salt bridges: D:R.37, D:R.37, D:K.47, D:K.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baumgartner, J. et al., Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme glucose-1-phosphate thymidylyltransferase (RfbA). Acta Crystallogr F Struct Biol Commun (2017)

Release Date

2012-04-04

Peptides

Glucose-1-phosphate thymidylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Glucose-1-phosphate thymidylyltransferase

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