1UBM	Oxidoreductase	date	Apr 04, 2003
title	Three-Dimensional Structure Of The Carbon Monoxide Complex O [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
authors	H.Ogata, Y.Mizoguchi, N.Mizuno, K.Miki, S.Adachi, N.Yasuoka, T.Yag O.Yamauchi, S.Hirota, Y.Higuchi
compound		source
Molecule: Periplasmic [Nife] Hydrogenase Small Subunit Chain: S Synonym: Small Subunit Of [Nife]Hydrogenase Ec: 1.12.2.1		Organism_scientific: Desulfovibrio Vulgaris Str. 'Miyazaki Organism_taxid: 883 Strain: Miyazaki F
Molecule: Periplasmic [Nife] Hydrogenase Large Subunit Chain: L Fragment: Residues 19-552 Synonym: Large Subunit Of [Nife]Hydrogenase Ec: 1.12.2.1		Organism_scientific: Desulfovibrio Vulgaris Str. 'Miyazaki Organism_taxid: 883 Strain: Miyazaki F
symmetry	Space Group: P 21 21 21	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 97.660 125.300 66.410 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.40 Å
ligand	F3S, FNE, MG, MPD, SF4	enzyme	Oxidoreductase E.C.1.12.2.1 BRENDA
related structures	by homologous chain: 1H2R, 1UBU
Gene Ontology	Chain Function Process Component L S
Primary reference	Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen., Ogata H, Mizoguchi Y, Mizuno N, Miki K, Adachi S, Yasuoka N, Yagi T, Yamauchi O, Hirota S, Higuchi Y, J Am Chem Soc 2002 Oct 2;124(39):11628-35. PMID:12296727

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (276 Kb) [Save to disk] Biological Unit Coordinates (1ubm.pdb1.gz) 269 Kb LPC: Ligand-Protein Contacts for 1UBM CSU: Contacts of Structural Units for 1UBM Likely Quarternary Molecular Structure file(s) for 1UBM Retrieve 1UBM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1UBM from S2C, [Save to disk]

View 1UBM 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 1UBM

Ramachandran plot from PDBSum

Structure-derived information

Conformational Epitope Prediction for 1UBM 1UBML 1UBMS from the CEP Server. Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1UBM, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1ubml_, region L [Jmol] [rasmolscript] [script source]     - Domain d1ubms_, region S [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: [1ubm] [1ubm_L] [1ubm_S] SWISS-PROT database: [P21852] [P21853] Domain organization of [PHNL_DESVM] [PHNS_DESVM] by SWISSPFAM

Other resources with information on 1UBM

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

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