SMTL ID : 7jxf.1

E. coli TSase complex with a bi-substrate reaction intermediate diastereomer analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

1 x 5HU: 5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE(Non-covalent)

5HU.1: 18 residues within 4Å: Chain A: R.21, W.80, Y.94, A.144, C.146, H.147, Q.165, R.166, S.167, C.168, D.169, G.173, N.177, H.207, Y.209 Chain B: R.126, R.127 Ligands: VMV.2 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.94, A:H.147, A:Q.165, A:S.167, A:D.169, A:N.177, A:N.177, A:Y.209, A:Y.209 Water bridges: A:C.146, B:R.126, B:R.126 Salt bridges: A:R.21, A:R.166, B:R.126, B:R.127

1 x VMV: N-[4-({[(6S)-2,4-diamino-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl]methyl}amino)benzene-1-carbonyl]-L-glutamic acid(Non-covalent)

VMV.2: 13 residues within 4Å: Chain A: K.48, I.79, W.83, L.143, D.169, L.172, G.173, Y.209, K.259, A.260, V.262, A.263 Ligands: 5HU.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.209, A:A.260, A:A.263, A:A.263 Water bridges: A:W.83 Salt bridges: A:K.48, A:D.169

3 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: H.108, I.109, D.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.110 Water bridges: A:H.108 NA.4: 3 residues within 4Å: Chain A: Q.64, F.240, D.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.64 NA.6: 4 residues within 4Å: Chain B: K.10, I.29, G.31, H.32 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:R.35, B:K.10 Hydrogen bonds: B:H.32

1 x VNM: (2S)-2-({4-[({(6S)-2,4-diamino-5-[(1-{(2R,4S,5R)-4-hydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)methyl]-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl}methyl)amino]benzoyl}amino)pentanedioic acid (non-preferred name)(Non-covalent)

VNM.5: 22 residues within 4Å: Chain A: R.126 Chain B: R.21, H.51, S.54, I.79, W.83, L.143, C.146, H.147, Q.165, R.166, S.167, C.168, D.169, L.172, G.173, F.176, N.177, H.207, Y.209, V.262, A.263 23 PLIP interactions: 20 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.79, B:L.172 Hydrogen bonds: B:H.51, B:Q.165, B:S.167, B:D.169, B:N.177, B:N.177, B:H.207, B:Y.209, B:A.263, B:A.263 Water bridges: B:R.21, B:S.54, B:Y.94, A:S.125, A:R.126 Salt bridges: B:R.21, B:K.48, B:R.166, B:D.169, A:R.126 pi-Stacking: B:F.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kholodar, S.A. et al., Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog. Biochemistry (2021)

Release Date

2021-04-21

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate synthase

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