1DML	Dna Binding Protein Transferase	date	Dec 14, 1999
title	Crystal Structure Of Herpes Simplex Ul42 Bound To The C-Term Hsv Pol
authors	H.J.Zuccola, D.J.Filman, D.M.Coen, J.M.Hogle
compound		source
Molecule: Dna Polymerase Processivity Factor Chain: A, C, E, G Fragment: N-Terminal Domain Synonym: Dna-Binding Protein Ul42 Engineered: Yes		Organism_scientific: Human Herpesvirus 1 Organism_common: Herpes Simplex Virus Type 1 Organism_taxid: 10298 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_plasmid: Pmal-C
Molecule: Dna Polymerase Chain: B, D, F, H Fragment: C-Terminal 36 Amino Acids Ec: 2.7.7.7 Engineered: Yes		Organism_scientific: Human Herpesvirus 1 Organism_common: Herpes Simplex Virus Type 1 Organism_taxid: 10298 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_plasmid: Pgex6p1
symmetry	Space Group: P 1 21 1	R_factor 0.230 R_Free 0.281
crystal cell	length a length b length c angle alpha angle beta angle gamma 54.320 100.070 129.530 90.00 100.62 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand		enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A, E, C, G F, B, H, D
Primary reference	The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase., Zuccola HJ, Filman DJ, Coen DM, Hogle JM, Mol Cell 2000 Feb;5(2):267-78. PMID:10882068

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (193 Kb) [Save to disk] Biological Unit Coordinates (1dml.pdb1.gz) 49 Kb Biological Unit Coordinates (1dml.pdb2.gz) 50 Kb Biological Unit Coordinates (1dml.pdb3.gz) 50 Kb Biological Unit Coordinates (1dml.pdb4.gz) 50 Kb CSU: Contacts of Structural Units for 1DML Likely Quarternary Molecular Structure file(s) for 1DML Structure Factors (539 Kb) Retrieve 1DML in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DML from S2C, [Save to disk] Re-refined 1dml structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1DML 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 1DML

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 1DML, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1dmla2, region A:170-319 [Jmol] [rasmolscript] [script source]     - Domain d1dmla1, region A:29-169 [Jmol] [rasmolscript] [script source]     - Domain d1dmlc2, region C:170-319 [Jmol] [rasmolscript] [script source]     - Domain d1dmlc1, region C:29-169 [Jmol] [rasmolscript] [script source]     - Domain d1dmle2, region E:170-319 [Jmol] [rasmolscript] [script source]     - Domain d1dmle1, region E:28-169 [Jmol] [rasmolscript] [script source]     - Domain d1dmlg2, region G:170-319 [Jmol] [rasmolscript] [script source]     - Domain d1dmlg1, region G:28-169 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1dml_E] [1dml_A] [1dml] [1dml_D] [1dml_H] [1dml_B] [1dml_G] [1dml_C] [1dml_F] SWISS-PROT database: [P07917] [P10226] Domain organization of [DPOL_HHV1A] [PAP_HHV11] by SWISSPFAM

Other resources with information on 1DML

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

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