Structure of PDB 4xyd Chain A

Receptor sequence

>4xydA (length=445) Species: 375451 (Roseobacter denitrificans OCh 114)

MKYQSQSIALVYFAVALGLFAIQVSGGLLLGWIYVSPNFLSEILPFNIVR
MLHTNSLIVWLLLGFMGAAYFVIPEESEREIHSPLLAYLQLAIMVLGTLG
VVVTYLFNLFEGNWLLGKEGREFLEQPVWVKMGIVVAALIFMYNISMTVL
QGRKTAITNVLLLGLWGLTLLFLFAFYNPSNLALDKMYWWYVVHLWVEGT
WELVMASVLAFLMLKLTGVDREIIEKWLYLIVATALFSGILGTGHHYFWI
GTPGYWQWIGSIFSALEVVPFFGMMAFAFVMVWKGRKDHPNKAALLWSLG
CATLAFFGAGVWGFLHTLHGINYYTHGTQITAAHGHLAFFGAYVSLNLAI
FSYAFPILRKRDPYNQVLNMASFWLMAGGMTFMTFVLTFAGTVQTHAQRV
QGDYFMDVQDAITIFYWMRFGSGIAVVLGALLFIYAVAVPRKEII

3D structure

• PDB: 4xyd Structure of the Membrane-intrinsic Nitric Oxide Reductase from Roseobacter denitrificans.
• Chain: A
• Resolution: 2.85 Å

Enzymatic activity

• Enzyme Commision number: 1.7.2.5: nitric-oxide reductase (cytochrome c).

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	HEM	A	Q23 V24 G27 L28 L30 Y34 R50 H53 L57 H336 F339 M380 R419	Q23 V24 G27 L28 L30 Y34 R50 H53 L57 H336 F339 M380 R419
BS02	HEM	A	E122 W190 V197 E198 H245 H246 E267 F271 A309 G313 F314 H316 T317 N322 H326 T331 H334 A338 F339 Y343	E122 W190 V197 E198 H245 H246 E267 F271 A309 G313 F314 H316 T317 N322 H326 T331 H334 A338 F339 Y343
BS03	FE	A	H194 E198 H245 H246	H194 E198 H245 H246
BS04	HEC	A	N47 M406	N47 M406

Gene Ontology

Molecular Function

• GO:0004129 cytochrome-c oxidase activity
• GO:0016491 oxidoreductase activity
• GO:0016966 nitric oxide reductase activity
• GO:0020037 heme binding
• GO:0046872 metal ion binding

Biological Process

• GO:0009060 aerobic respiration
• GO:0015990 electron transport coupled proton transport
• GO:0022904 respiratory electron transport chain

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:4xyd, PDBe:4xyd, PDBj:4xyd
• PDBsum: 4xyd
• PubMed: 27185533
• UniProt: Q16A04