SMTL ID : 1b5d.1 (1 other biounit)

DCMP Hydroxymethylase from T4 (Intact)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x DCM: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DCM.1: 13 residues within 4Å: Chain A: K.28, Y.96, C.148, R.168, S.169, N.170, D.171, G.175, D.179, H.216, Y.218 Chain B: R.123, R.124 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.96, A:S.169, A:N.170, A:D.171, A:D.179, A:H.216, A:Y.218 Water bridges: A:R.168, B:R.123, B:R.124 Salt bridges: A:K.28, A:R.168, B:R.123, B:R.124 DCM.2: 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, D.179, H.216, Y.218 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.96, B:S.169, B:N.170, B:D.171, B:D.179, B:H.216 Water bridges: B:R.168, A:R.124 Salt bridges: B:K.28, B:R.168, A:R.123, A:R.124 DCM.3: 13 residues within 4Å: Chain C: K.28, Y.96, C.148, R.168, S.169, N.170, D.171, G.175, D.179, H.216, Y.218 Chain D: R.123, R.124 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:S.169, C:N.170, C:D.171, C:D.179, C:H.216 Water bridges: C:R.168, D:R.123, D:R.124 Salt bridges: C:K.28, C:R.168, D:R.123, D:R.124 DCM.4: 13 residues within 4Å: Chain C: R.123, R.124 Chain D: K.28, Y.96, C.148, R.168, S.169, N.170, D.171, G.175, D.179, H.216, Y.218 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.169, D:N.170, D:D.171, D:D.179, D:H.216, D:Y.218 Water bridges: D:R.168, C:R.124 Salt bridges: D:K.28, D:R.168, C:R.123, C:R.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, H.K. et al., Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex. EMBO J. (1999)

Release Date

1999-01-13

Peptides

PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE)

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