Structure of PDB 1qdb Chain B

Receptor sequence

>1qdbB (length=473) Species: 65553 (Sulfurospirillum deleyianum)

GIAGKEKSEEWAKYYPRQFDSWKKTKEYDSFTDMLAKDPALVIAWSGYAF
SKDYNSPRGHYYALQDNVNSLRTGAPVDAKTGPLPTACWTCKSPDVPRLI
EEDGELEYFTGKWAKYGSQIVNVIGCANCHDDKTAELKVRVPHLNRGLQA
AGLKTFEESTHQDKRTLVCAQCHVEYYFKKTEWKDAKGADKTAMVVTLPW
ANGVGKDGNAGVEGMIKYYDEINFSDWTHNISKTPMLKAQHPGFEFWKSG
IHGQKGVSCADCHMPYTQEGSVKYSDHQVKENPLDSMDQSCMNCHRESES
KLRGIVHQKYERKEFLNKVAFDNIGKAHLETGKAIEAGASDEELKEVRKL
IRHGQFKADMAIAAHGNYFHAPEETLRLLAAGSDDAQKARLLLVKILAKH
GVMDYIAPDFDTKDKAQKLAKVDIAALAAEKMKFKQTLEQEWKKEAKAKG
RANPELYKDVDTINDGKSSWNKK

3D structure

• PDB: 1qdb Structure of cytochrome c nitrite reductase.
• Chain: B
• Resolution: 1.9 Å

Enzymatic activity

• Enzyme Commision number: 1.7.2.2: nitrite reductase (cytochrome; ammonia-forming).

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	CA	B	E216 Y217 K279 Q281	E175 Y176 K238 Q240
BS02	HEC	B	N96 P98 N108 R113 C129 C132 K133 C213 H214 Y217 F219 H282	N55 P57 N67 R72 C88 C91 K92 C172 H173 Y176 F178 H241
BS03	HEC	B	Y56 Q59 W63 G166 C167 C170 H171 L178 H202 R206 M305 S316 H318	Y15 Q18 W22 G125 C126 C129 H130 L137 H161 R165 M264 S275 H277
BS04	HEC	B	R99 G100 H101 Y103 A104 D107 C132 K133 I165 C210 Q212 C213 H214 H304 V320 K321 E322	R58 G59 H60 Y62 A63 D66 C91 K92 I124 C169 Q171 C172 H173 H263 V279 K280 E281
BS05	HEC	B	H214 W288 H293 S299 C300 C303 H304 E322 N323 P324 H406 G407 Y409 F410 H411	H173 W247 H252 S258 C259 C262 H263 E281 N282 P283 H365 G366 Y368 F369 H370
BS06	HEC	B	I292 H293 K296 V298 S331 C332 C335 H336 L343 K350 F410	I251 H252 K255 V257 S290 C291 C294 H295 L302 K309 F369

Gene Ontology

Molecular Function

• GO:0005509 calcium ion binding
• GO:0016491 oxidoreductase activity
• GO:0020037 heme binding
• GO:0042279 nitrite reductase (cytochrome, ammonia-forming) activity
• GO:0046872 metal ion binding

Biological Process

• GO:0019645 anaerobic electron transport chain
• GO:0042128 nitrate assimilation

Cellular Component

• GO:0030288 outer membrane-bounded periplasmic space
• GO:0042597 periplasmic space

External links

• PDB: RCSB:1qdb, PDBe:1qdb, PDBj:1qdb
• PDBsum: 1qdb
• PubMed: 10440380
• UniProt: Q9Z4P4|NRFA_SULDE Cytochrome c-552 (Gene Name=nrfA)