Structure of PDB 5mdl Chain S

Receptor sequence

>5mdlS (length=269) Species: 381666 (Cupriavidus necator H16)

PRTPVLWLHGLECTCCSESFIRSAHPLAKDVVLSMISLDYDDTLMAAAGH
QAEAILEEIMTKYKGNYILAVEGNPPLNQDGMSCIIGGRPFIEQLKYVAK
DAKAIISWGSCASWGCVQAAKPNPTQATPVHKVITDKPIIKVPGCPPIAE
VMTGVITYMLTFDRIPELDRQGRPKMFYSQRIHDKCYRRPHFDAGQFVEE
WDDESARKGFCLYKMGCKGPTTYNACSTTRWNEGTSFPIQSGHGCIGCSE
DGFWDKGSFYDRLTGISQF

3D structure

• PDB: 5mdl Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase.
• Chain: S
• Resolution: 1.41 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	S	H187 C190 R192 R193 C215 L216 Y217 C221 P224 I243	H183 C186 R188 R189 C211 L212 Y213 C217 P220 I239
BS02	F3S	S	C230 W235 P242 C249 I250 C252	C226 W231 P238 C245 I246 C248
BS03	F4S	S	C17 T18 C19 C20 E76 C115 C120 C149	C13 T14 C15 C16 E72 C111 C116 C145
BS04	OXY	S	S21 E22 I25	S17 E18 I21

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• 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:0005886 plasma membrane
• GO:0009375 ferredoxin hydrogenase complex
• GO:0016020 membrane
• GO:0044569 [Ni-Fe] hydrogenase complex

External links

• PDB: RCSB:5mdl, PDBe:5mdl, PDBj:5mdl
• PDBsum: 5mdl
• PubMed: 29463722
• UniProt: P31892|MBHS_CUPNH Uptake hydrogenase small subunit (Gene Name=hoxK)