A Hydrophilic Channel Is Involved in Oxidative Inactivation of a [NiFeSe] Hydrogenase
Zacarias, S., Temporao, A., del Barrio, M., Fourmond, V., Leger, C., Matias, P.M., Pereira, I.A.C.(2019) ACS Catal 
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
(2019) ACS Catal 
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Periplasmic [NiFeSe] hydrogenase, small subunit | 283 | Nitratidesulfovibrio vulgaris str. Hildenborough | Mutation(s): 0  Gene Names: hysB, DVU_1917 EC: 1.12.7.2 | ||
UniProt | |||||
Find proteins for Q72AS4 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72AS4  Go to UniProtKB:  Q72AS4 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q72AS4 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing | 492 | Nitratidesulfovibrio vulgaris str. Hildenborough | Mutation(s): 1  Gene Names: hysA, DVU_1918 EC: 1.12.7.2 | ||
UniProt | |||||
Find proteins for Q72AS3 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72AS3  Go to UniProtKB:  Q72AS3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q72AS3 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 8 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
6ML Query on 6ML | F [auth A] | oxygen-damaged SF4 Fe4 O2 S4 DCVJTSMMUVGUAG-UHFFFAOYSA-M | |||
SF4 Query on SF4 | C [auth A], D [auth A], E [auth A] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N | |||
FCO Query on FCO | H [auth B] | CARBONMONOXIDE-(DICYANO) IRON C3 Fe N2 O VBQUCMTXYFMTTE-UHFFFAOYSA-N | |||
GOL Query on GOL | G [auth A], M [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
NI Query on NI | I [auth B] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N | |||
FE2 Query on FE2 | J [auth B] | FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N | |||
CL Query on CL | L [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
H2S Query on H2S | K [auth B] | HYDROSULFURIC ACID H2 S RWSOTUBLDIXVET-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
CSD Query on CSD | B | L-PEPTIDE LINKING | C3 H7 N O4 S | CYS |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 105.41 | α = 90 |
b = 63.589 | β = 104.88 |
c = 110.705 | γ = 90 |
Software Name | Purpose |
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PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
Funding Organization | Location | Grant Number |
---|---|---|
Fundacao para a Ciencia e a Tecnologia | Portugal | PTDC/BBB-BEP/2885/2014 |
Fundacao para a Ciencia e a Tecnologia | Portugal | SFRH/BD/100314/2014 |