2frv Summary

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CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE

The structure was published by Volbeda, A., Garcin, E., Piras, C., et al., Hatchikian, E.C., Frey, M., and Fontecilla-Camps, J.C., in 1996 in a paper entitled "Structure of the [Nife] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.54 Å and deposited in 1997.

The experimental data on which the structure is based was not deposited.

This PDB entry contains a complex of 2 biomacromolecules, namely PERIPLASMIC HYDROGENASE.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
S PERIPLASMIC HYDROGENASE P12943 (25-288) (PHNS_DESGI)search Desulfovibrio gigassearch 100% 264 98%
A PERIPLASMIC HYDROGENASE P12943 (25-288) (PHNS_DESGI)search Desulfovibrio gigassearch 100% 264 98%
C PERIPLASMIC HYDROGENASE P12943 (25-288) (PHNS_DESGI)search Desulfovibrio gigassearch 100% 264 98%
E PERIPLASMIC HYDROGENASE P12943 (25-288) (PHNS_DESGI)search Desulfovibrio gigassearch 100% 264 98%
G PERIPLASMIC HYDROGENASE P12943 (25-288) (PHNS_DESGI)search Desulfovibrio gigassearch 100% 264 98%
I PERIPLASMIC HYDROGENASE P12943 (25-288) (PHNS_DESGI)search Desulfovibrio gigassearch 100% 264 98%
L PERIPLASMIC HYDROGENASE P12944 (1-536) (PHNL_DESGI)search Desulfovibrio gigassearch 97% 536 98%
B PERIPLASMIC HYDROGENASE P12944 (1-536) (PHNL_DESGI)search Desulfovibrio gigassearch 97% 536 98%
D PERIPLASMIC HYDROGENASE P12944 (1-536) (PHNL_DESGI)search Desulfovibrio gigassearch 97% 536 98%
F PERIPLASMIC HYDROGENASE P12944 (1-536) (PHNL_DESGI)search Desulfovibrio gigassearch 97% 536 98%
H PERIPLASMIC HYDROGENASE P12944 (1-536) (PHNL_DESGI)search Desulfovibrio gigassearch 97% 536 98%
J PERIPLASMIC HYDROGENASE P12944 (1-536) (PHNL_DESGI)search Desulfovibrio gigassearch 97% 536 98%


This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
P12943 (25 - 288) PERIPLASMIC HYDROGENASE Desulfovibrio gigas
P12944 (1 - 536) PERIPLASMIC HYDROGENASE Desulfovibrio gigas

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
S, A, C, E, G, I (P12943) Nickel-iron hydrogenase, small subunitsearch Rossmann foldsearch, Cytochrome-c3 Hydrogenase, chain A, domain 2search PF01058: NADH ubiquinone oxidoreductase, 20 Kd subunitsearch, PF14720: NiFe/NiFeSe hydrogenase small subunit C-terminalsearch
L, B, D, F, H, J (P12944) Nickel-iron hydrogenase, large subunitsearch Cytochrome-c3 Hydrogenase, chain Bsearch PF00374: Nickel-dependent hydrogenasesearch

Chain ID Biological process (GO) Molecular function (GO) Cellular component (GO)
S, A, C, E, G, I (P12943) oxidation-reduction processsearch ferredoxin hydrogenase activitysearch iron-sulfur cluster bindingsearch oxidoreductase activitysearch 4 iron, 4 sulfur cluster bindingsearch cytochrome-c3 hydrogenase activitysearch metal ion bindingsearch 3 iron, 4 sulfur cluster bindingsearch ferredoxin hydrogenase complexsearch periplasmic spacesearch
L, B, D, F, H, J (P12944) oxidation-reduction processsearch ferredoxin hydrogenase activitysearch metal ion bindingsearch oxidoreductase activitysearch nickel cation bindingsearch cytochrome-c3 hydrogenase activitysearch periplasmic spacesearch

Chain InterPro annotation
S, A, C, E, G, I [NiFe]-hydrogenase, small subunitsearch NADH:ubiquinone oxidoreductase-like, 20kDa subunitsearch Cytochrome-c3 hydrogenase, C-terminalsearch
L, B, D, F, H, J Nickel-dependent hydrogenase, large subunitsearch Nickel-dependent hydrogenase, large subunit, nickel binding sitesearch NiFe hydrogenase-likesearch