SMTL ID : 6l18.1

XFEL structure of T4dCH D179N mutant complex with natively expressed dTMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.1: 13 residues within 4Å: Chain A: K.28, Y.96, C.148, R.168, S.169, N.170, D.171, G.175, N.179, H.216, Y.218 Chain B: R.123, R.124 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Y.96, A:S.169, A:N.170, A:D.171, A:N.179, A:N.179, A:Y.218, A:Y.218 Water bridges: A:T.149, B:R.123, B:R.124, B:R.124 Salt bridges: A:K.28, A:R.168, B:R.123, B:R.124 TMP.4: 13 residues within 4Å: Chain A: R.123, R.124 Chain B: K.28, Y.96, C.148, R.168, S.169, N.170, D.171, G.175, N.179, H.216, Y.218 16 PLIP interactions: 5 interactions with chain A, 11 interactions with chain B Water bridges: A:R.123, A:R.124, A:R.124, B:T.149 Salt bridges: A:R.123, A:R.124, B:K.28, B:R.168 Hydrogen bonds: B:Y.96, B:S.169, B:N.170, B:D.171, B:N.179, B:N.179, B:Y.218, B:Y.218

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: T.78, Q.83 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain B: T.78, Q.83 Ligand excluded by PLIP

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

NA.3: 4 residues within 4Å: Chain A: K.72, I.74, G.76, T.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.72, A:T.78 Water bridges: A:T.78 NA.6: 4 residues within 4Å: Chain B: K.72, I.74, G.76, T.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.78, B:T.78 Water bridges: B:T.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, S.H. et al., A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser. Sci Rep (2019)

Release Date

2019-12-04

Peptides

Deoxycytidylate 5-hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Deoxycytidylate 5-hydroxymethyltransferase