1B5D	Transferase	date	Jan 06, 1999
title	Dcmp Hydroxymethylase From T4 (Intact)
authors	H.K.Song, S.H.Sohn, S.W.Suh
compound		source
Molecule: Protein (Deoxycytidylate Hydroxymethylase) Chain: A, B Synonym: Deoxycytidylate Hydroxymethylase, Dcmp Hydroxymeth Ec: 2.1.2.8		Organism_scientific: Enterobacteria Phage T4 Organism_taxid: 10665
symmetry	Space Group: C 1 2 1	R_factor 0.160 R_Free 0.208
crystal cell	length a length b length c angle alpha angle beta angle gamma 176.230 53.290 75.860 90.00 115.54 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	DCM	enzyme	Transferase E.C.2.1.2.8 BRENDA
related structures	by homologous chain: 1B49, 1B5E
Gene Ontology	Chain Function Process Component A, B
Primary reference	Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex., Song HK, Sohn SH, Suh SW, EMBO J 1999 Mar 1;18(5):1104-13. PMID:10064578

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (87 Kb) [Save to disk] Biological Unit Coordinates (1b5d.pdb1.gz) 165 Kb Biological Unit Coordinates (1b5d.pdb2.gz) 83 Kb LPC: Ligand-Protein Contacts for 1B5D CSU: Contacts of Structural Units for 1B5D Likely Quarternary Molecular Structure file(s) for 1B5D Structure Factors (221 Kb) Retrieve 1B5D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1B5D from S2C, [Save to disk] Re-refined 1b5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1B5D in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1B5D

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1B5D, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1b5da_, region A [Jmol] [rasmolscript] [script source]     - Domain d1b5db_, region B [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1b5d_A] [1b5d_B] [1b5d] SWISS-PROT database: [P08773] Domain organization of [DCHM_BPT4] by SWISSPFAM

Other resources with information on 1B5D

Community annotation for 1B5D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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