Structure of PDB 5xvd Chain T

Receptor sequence

>5xvdT (length=269) Species: 1686381 (Citrobacter sp. MGH106)

PQRPPVIWIGAQECTGCTESLLRATHPTVENLVLETISLEYHEVLSAAFG
HQVEENKHNALEKYKGQYVLVVDGSIPLKDNGIYCMVAGEPIVDHIRRAA
EGAAAIIAIGSCAAWGGVAAAGVNPTGAVGLQEVLPGKTIINIPGCPPNP
HNFLATVAHIITYGKPPKLDAKNRPTFAYGRLIHEHCERRPHFDAGRFAK
EFGDEGHREGWCLYHLGCKGPETYGNCSTLQFCDVGGVWPVAIGHPCYGC
NEEGIGFHKGIHQLAHVEN

3D structure

• PDB: 5xvd Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2.
• Chain: T
• Resolution: 1.57 Å

Enzymatic activity

• Enzyme Commision number: 1.12.99.6: hydrogenase (acceptor).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	SF4	T	H192 C195 R197 R198 C220 L221 Y222 C226 P229	H184 C187 R189 R190 C212 L213 Y214 C218 P221
BS02	F3S	T	I191 C235 F240 P248 C255 Y256 G257 C258 N259	I183 C227 F232 P240 C247 Y248 G249 C250 N251
BS03	SF4	T	E21 C22 G24 C25 C120 C154	E13 C14 G16 C17 C112 C146
BS04	8JU	T	C22 T23 G24 C25 G118 C120 C154 P155	C14 T15 G16 C17 G110 C112 C146 P147

Gene Ontology

Molecular Function

• GO:0008901 ferredoxin hydrogenase activity
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0033748 hydrogenase (acceptor) activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051538 3 iron, 4 sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0009061 anaerobic respiration

Cellular Component

• GO:0009375 ferredoxin hydrogenase complex
• GO:0016020 membrane
• GO:0044569 [Ni-Fe] hydrogenase complex

External links

• PDB: RCSB:5xvd, PDBe:5xvd, PDBj:5xvd
• PDBsum: 5xvd
• PubMed: 30328414
• UniProt: A0A0J1PJ79