SMTL ID : 6a9b.1

T4 dCMP hydroxymethylase structure solved by I-SAD using a home source

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

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

IOD.1: 3 residues within 4Å: Chain A: K.72, T.78, Q.83 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain B: K.72, T.78, Q.83 Ligand excluded by PLIP

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: K.28, R.168, S.169 Chain B: R.123, R.124 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Water bridges: B:S.122, B:R.123, B:R.123, B:R.124 Salt bridges: B:R.123, B:R.124, A:K.28, A:R.168 Hydrogen bonds: A:S.169 PO4.4: 5 residues within 4Å: Chain A: R.123, R.124 Chain B: K.28, R.168, S.169 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Water bridges: A:S.122, A:R.123, A:R.123, A:R.124 Salt bridges: A:R.123, A:R.124, B:K.28, B:R.168 Hydrogen bonds: B:S.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, S.H. et al., A cytosine modification mechanism revealed by the structure of a ternary complex of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate. Iucrj (2019)

Release Date

2019-01-02

Peptides

Deoxycytidylate 5-hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Deoxycytidylate 5-hydroxymethyltransferase

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