OCA Atlas for 1VH8

1VH8

Lyase

date

Dec 01, 2003

title

Crystal Structure Of A 2c-Methyl-D-Erythritol 2,4-Cyclodipho Synthase

authors

Structural Genomix

compound

source

Molecule: 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synt
Chain: A, B, C, D, E, F
Synonym: Mecps, Mecdp-Synthase
Ec: 4.6.1.12
Engineered: Yes

Organism_scientific: Haemophilus Influenzae
Organism_taxid: 727
Gene: Ispf, Hi0671
Expression_system: Escherichia Coli
Expression_system_taxid: 562

symmetry

Space Group: I 41

R_factor

0.240

R_Free

0.280

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
104.850	104.850	195.750	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.35 Å

ligand

ACY, MSE, POP

enzyme

Lyase E.C.4.6.1.12 BRENDA

related structures

by homologous chain: 1H48, 1VHA

Gene
Ontology

Chain	Function	Process	Component
F, A, D, C, E, B

Primary reference

Structural analysis of a set of proteins resulting from a bacterial genomics project., Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ, Proteins 2005 Sep 1;60(4):787-96. PMID:16021622

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]

Biological Unit Coordinates (1vh8.pdb1.gz) 74 Kb

Biological Unit Coordinates (1vh8.pdb2.gz) 73 Kb

Biological Unit Coordinates (1vh8.pdb3.gz) 285 Kb

LPC: Ligand-Protein Contacts for 1VH8

CSU: Contacts of Structural Units for 1VH8

Likely Quarternary Molecular Structure file(s) for 1VH8

Structure Factors (975 Kb)

Retrieve 1VH8 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1VH8 from S2C, [Save to disk]

Re-refined 1vh8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1VH8 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 1VH8

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 1VH8, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1vh8a_, region A [Jmol] [rasmolscript] [script source]
- Domain d1vh8b_, region B [Jmol] [rasmolscript] [script source]
- Domain d1vh8c_, region C [Jmol] [rasmolscript] [script source]
- Domain d1vh8d_, region D [Jmol] [rasmolscript] [script source]
- Domain d1vh8e_, region E [Jmol] [rasmolscript] [script source]
- Domain d1vh8f_, region F [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: [1vh8_A] [1vh8_F] [1vh8] [1vh8_D] [1vh8_E] [1vh8_B] [1vh8_C]

SWISS-PROT database: [P44815]

Domain organization of [ISPF_HAEIN] by SWISSPFAM

Other resources with information on 1VH8

Community annotation for 1VH8 at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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