SMTL ID : 1iim.1

thymidylyltransferase complexed with TTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

8 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 18 residues within 4Å: Chain A: L.9, A.10, G.11, G.12, S.13, G.14, T.15, R.16, Q.26, Q.27, Q.83, P.86, D.87, G.88, L.89, L.109, G.110, D.111 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.89 Hydrogen bonds: A:G.11, A:S.13, A:S.13, A:G.14, A:T.15, A:R.16, A:R.16, A:Q.83, A:Q.83, A:G.88, A:G.110, A:D.111, A:D.111 Water bridges: A:G.12 Salt bridges: A:R.16 TTP.2: 15 residues within 4Å: Chain A: L.46, Y.115, G.116, H.117, D.118, L.119, P.120, V.251, S.252, E.256, I.257, R.260 Chain B: G.219, R.220, G.221 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.46 Hydrogen bonds: A:G.116, A:G.116, A:D.118, A:S.252, B:R.220, B:G.221 Water bridges: A:K.250, B:G.219, B:G.219, B:R.220, B:R.220 Salt bridges: A:H.117 pi-Cation interactions: B:R.220 TTP.3: 15 residues within 4Å: Chain A: G.219, R.220, G.221 Chain B: L.46, Y.115, G.116, H.117, D.118, L.119, P.120, V.251, S.252, E.256, I.257, R.260 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:R.220, A:G.221, B:G.116, B:G.116, B:D.118, B:S.252 Water bridges: A:G.219, A:R.220, A:R.220, A:R.220, B:H.117, B:D.118, B:K.250 pi-Cation interactions: A:R.220 Hydrophobic interactions: B:L.46 Salt bridges: B:H.117 TTP.4: 17 residues within 4Å: Chain B: L.9, G.11, G.12, S.13, G.14, T.15, R.16, Q.26, Q.27, Q.83, P.86, D.87, G.88, L.89, L.109, G.110, D.111 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.89 Hydrogen bonds: B:G.11, B:G.12, B:S.13, B:G.14, B:T.15, B:R.16, B:Q.83, B:Q.83, B:G.88, B:G.110, B:D.111, B:D.111 Water bridges: B:G.12, B:R.16, B:Q.26 Salt bridges: B:R.16 TTP.5: 18 residues within 4Å: Chain C: L.9, A.10, G.11, G.12, S.13, G.14, T.15, R.16, Q.26, Q.27, Q.83, P.86, D.87, G.88, L.89, L.109, G.110, D.111 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:L.89 Hydrogen bonds: C:G.11, C:S.13, C:S.13, C:G.14, C:T.15, C:R.16, C:R.16, C:Q.83, C:Q.83, C:G.88, C:G.110, C:D.111, C:D.111 Water bridges: C:G.12, C:T.15, C:T.15 Salt bridges: C:R.16 TTP.6: 15 residues within 4Å: Chain C: L.46, Y.115, G.116, H.117, D.118, L.119, P.120, V.251, S.252, E.256, I.257, R.260 Chain D: G.219, R.220, G.221 15 PLIP interactions: 8 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:L.46 Hydrogen bonds: C:G.116, C:G.116, C:D.118, C:S.252, D:R.220, D:G.221 Water bridges: C:D.118, C:K.250, D:G.219, D:G.219, D:R.220, D:R.220 Salt bridges: C:H.117 pi-Cation interactions: D:R.220 TTP.7: 15 residues within 4Å: Chain C: G.219, R.220, G.221 Chain D: L.46, Y.115, G.116, H.117, D.118, L.119, P.120, V.251, S.252, E.256, I.257, R.260 16 PLIP interactions: 9 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:L.46 Hydrogen bonds: D:Y.115, D:G.116, D:G.116, D:D.118, D:S.252, C:R.220, C:G.221 Water bridges: D:H.117, D:K.250, C:G.219, C:R.220, C:R.220, C:R.220 Salt bridges: D:H.117 pi-Cation interactions: C:R.220 TTP.8: 17 residues within 4Å: Chain D: L.9, G.11, G.12, S.13, G.14, T.15, R.16, Q.26, Q.27, Q.83, P.86, D.87, G.88, L.89, L.109, G.110, D.111 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.89 Hydrogen bonds: D:G.11, D:G.12, D:S.13, D:G.14, D:T.15, D:R.16, D:Q.83, D:Q.83, D:G.88, D:G.110, D:D.111, D:D.111 Water bridges: D:G.12, D:R.16, D:Q.26 Salt bridges: D:R.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barton, W.A. et al., Structure, mechanism and engineering of a nucleotidylyltransferase as a first step toward glycorandomization. Nat.Struct.Biol. (2001)

Release Date

2001-05-09

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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