SMTL ID : 6n0u.1 (1 other biounit)

Crystal structure of a glucose-1-phosphate thymidylyltransferase from Burkholderia phymatum bound to 2'-deoxy-thymidine-B-L-rhamnose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x TRH: 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE(Non-covalent)

TRH.1: 25 residues within 4Å: Chain A: L.16, G.18, G.19, Q.34, Q.90, P.93, D.94, G.95, L.96, L.116, D.118, R.152, Y.153, G.154, E.169, K.170, V.180, T.181, G.182, Y.184, R.202, E.204, I.207, T.208, W.231 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.116, A:Y.153, A:W.231 Hydrogen bonds: A:G.18, A:Q.34, A:Q.90, A:Q.90, A:G.95, A:D.118, A:G.154, A:E.169, A:K.170, A:Y.184 Water bridges: A:G.19, A:G.19, A:G.117, A:E.206, A:T.208 Salt bridges: A:K.170, A:K.170, A:R.202 TRH.3: 26 residues within 4Å: Chain B: L.16, G.18, G.19, S.20, Q.34, Q.90, P.93, D.94, G.95, L.96, L.116, D.118, R.152, Y.153, G.154, E.169, K.170, V.180, T.181, G.182, Y.184, R.202, E.204, I.207, T.208, W.231 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:L.96, B:L.116, B:Y.153, B:W.231 Hydrogen bonds: B:G.18, B:Q.34, B:Q.90, B:Q.90, B:G.95, B:D.118, B:G.154, B:E.169, B:K.170, B:T.208 Water bridges: B:L.96, B:G.117, B:D.118, B:R.152, B:R.202, B:R.202, B:T.208 Salt bridges: B:K.170, B:K.170, B:K.170, B:R.202 TRH.4: 25 residues within 4Å: Chain C: L.16, G.18, G.19, Q.34, Q.90, P.93, D.94, G.95, L.96, L.116, D.118, R.152, Y.153, G.154, E.169, K.170, V.180, T.181, G.182, Y.184, R.202, E.204, I.207, T.208, W.231 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:L.116, C:Y.153, C:W.231 Hydrogen bonds: C:G.18, C:Q.34, C:Q.90, C:Q.90, C:G.95, C:D.118, C:G.154, C:E.169, C:K.170, C:T.208 Water bridges: C:G.19, C:G.19, C:G.117, C:R.202, C:T.208 Salt bridges: C:K.170, C:K.170, C:R.202 TRH.6: 26 residues within 4Å: Chain D: L.16, G.18, G.19, S.20, Q.34, Q.90, P.93, D.94, G.95, L.96, L.116, D.118, R.152, Y.153, G.154, E.169, K.170, V.180, T.181, G.182, Y.184, R.202, E.204, I.207, T.208, W.231 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:L.96, D:L.116, D:Y.153, D:W.231 Hydrogen bonds: D:G.18, D:Q.34, D:Q.90, D:Q.90, D:G.95, D:D.118, D:G.154, D:E.169, D:K.170, D:Y.184 Water bridges: D:G.117, D:D.118, D:R.152, D:R.202, D:R.202, D:E.206, D:T.208 Salt bridges: D:K.170, D:K.170, D:K.170, D:R.202

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: G.123, H.124, D.125, L.126, A.127 Chain B: G.228 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.125, A:L.126, A:A.127, B:G.228 EDO.5: 6 residues within 4Å: Chain C: G.123, H.124, D.125, L.126, A.127 Chain D: G.228 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.125, C:L.126, C:A.127, D:G.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edwards, T.E. et al., Crystal structure of a glucose-1-phosphate thymidylyltransferase from Burkholderia phymatum bound to 2'-deoxy-thymidine-B-L-rhamnose. To Be Published

Release Date

2018-11-21

Peptides

Glucose-1-phosphate thymidylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glucose-1-phosphate thymidylyltransferase

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