1DY7A

Cytochrome cd1 nitrite reductase, co complex
Total Genus 129
50100150200250300350400020406080100120
Genus TraceResidueGenus

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
129
sequence length
434
structure length
434
Chain Sequence
PPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY
50100150200250300350400400300200100
020406080100120Genus Matrix

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
EMPTYTI15 (421-424)S2 (168-173)TII3 (427-430)S26 (430-436)3H2 (165-167)S1 (147-148)TIV2 (196-199)3H1 (152-154)TVIII1 (148-151)TI1 (183-186)TIV1 (156-159)TI3 (205-208)TVIII2 (227-230)S6 (210-215)3H3 (174-176)S3 (178-183)TVIII3 (239-242)TI5 (224-227)TI2 (184-187)S4 (189-194)S5 (199-204)S10 (257-264)S7 (219-224)TI4 (215-218)S8 (231-237)TII1 (250-253)TI6 (272-275)S12 (278-283)TIV5 (273-276)TII2 (253-256)O1 (309-311)TIV4 (263-266)S19 (344-349)S11 (267-272)S14 (294-295)S13 (286-287)TIV8 (306-309)TIV6 (288-291)TI7 (289-292)TIV7 (295-298)S15 (300-306)S17 (321-326)S16 (311-316)S22 (375-381)TI9 (317-320)TI8 (316-319)TIV10 (341-344)S24 (401-408)S18 (335-339)TI12 (371-374)TVIII5 (327-330)TIV11 (370-373)TIV9 (330-333)TI10 (329-332)TI11 (350-353)S20 (355-360)3H4 (361-363)S25 (413-418)TIV14 (420-423)TIV12 (384-387)3H5 (425-427)TIV13 (397-400)S23 (387-397)TI14 (408-411)S21 (365-370)AH1 (139-145)S9 (241-247)Updating...
connected with : NaN
molecule tags Oxidoreductase
publication title Proton-Coupled Structural Changes Upon Binding of Carbon Monoxide to Cytochrome Cd(1): A Combined Flash Photolysis and X-Ray Crystallography Study
pubmed doi rcsb
molecule keywords NITRITE REDUCTASE
total genus 129
structure length 434
sequence length 434
chains with identical sequence B
ec nomenclature ec 1.7.2.1: Nitrite reductase (NO-forming).
pdb deposition date 2000-01-28

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF02239 Cytochrom_D1 Cytochrome D1 heme domain
A PF13442 Cytochrome_CBB3 Cytochrome C oxidase, cbb3-type, subunit III
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.140.10.20 Mainly Beta 8 Propeller Methanol Dehydrogenase; Chain A C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase 1dy7A00
1HJ5A 1HJ4A 1HZVA 1E2RA 1GQ1A 1GJQA 1NIRA 1HCMA 1QKSA 1NNOA 1N50A 1N15A 1DY7A 1H9XA 1HZUA 1H9YA 1AOMA 1N90A 1BL9A 1HJ3A 1AOQA 1AOFA
chains in the Genus database with same CATH superfamily
2GBIA 3VJLA 3D4LA 3OPMA 1H4IA 4N8DA 4PNZA 1GQ1A 3KWJA 1QKSA 3O9VA 4AAHA 3G0BA 3SX4A 1R9NA 1KV9A 5I7UA 1W6SA 1WCYA 1N15A 4JH0A 2G63A 1H9XA 2QTBA 2BUAA 2AJCA 3WQHA 2IIVA 4MAEA 2BGNA 1AOMA 2RGUA 5T4EA 4WJLA 2BGRA 5T4HA 2OAGA 5J3JA 3Q0TA 1HJ3A 4N8EA 4DTCA 3C45A 3SWWA 1NU6A 1RWQA 3G0GA 2OPHA 1HCMA 3VJKA 4CVCA 2AJ8A 1NNOA 5KBYA 3EIOA 4QZVA 2AJBA 4PV7A 2ONCA 1DY7A 2OQVA 3QBJA 2FJPA 2I3ZA 3KWFA 3O95A 2BUBA 5T4BA 2RIPA 1H4JA 1H9YA 1LRWA 3OC0A 4KR0A 4G1FA 3F8SA 2QJRA 4DSZA 3CCCA 4A5SA 1TK3A 4LKOA 2G5PA 2AD7A 1U8EA 2JIDA 1HJ5A 2GBGA 4DSAA 3H0CA 1ORVA 4FFWA 4J3JA 1HZVA 1E2RA 1GJQA 3G0DA 5ISMA 1PFQA 1NIRA 2QT9A 2DCMA 2EEPA 1N50A 3VJMA 1TKRA 2Z3WA 1FLGA 3C43A 4MH1A 1XFDA 1N1MA 2I78A 2D0VA 4FFVA 2Z3ZA 3BJMA 1AOQA 1AOFA 1Z68A 2I03A 2P8SA 4CVBA 1HJ4A 2HHAA 1ORWA 2GBFA 1KB0A 2GBCA 2IITA 1X70A 2QOEA 3HABA 2BUCA 1NU8A 2OAEA 2ECFA 5LLSA 3W2TA 1R9MA 2AD8A 5T4FA 1HZUA 3NOXA 2OGZA 2OLEA 1W1IA 3HACA 4TQOA 1N90A 3CCBA 3G0CA 4Q1VA 2AJDA 2D5LA 1J2EA 1BL9A 3Q8WA 1YIQA 4L72A 1G72A 2AJLI 2QKYA 2OQIA 2AD6A 2G5TA
chains in the Genus database with same CATH topology
1HJ5A 1HJ4A 1HZVA 1E2RA 1GQ1A 1GJQA 1NIRA 1HCMA 1QKSA 1NNOA 1N50A 1N15A 1DY7A 1H9XA 1HZUA 1H9YA 1AOMA 1N90A 1BL9A 1HJ3A 1AOQA 1AOFA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1HJ5 A;  1HJ4 A;  1HZV A;  1E2R A;  1GQ1 A;  1GJQ A;  1NIR A;  1HCM A;  1QKS A;  1NNO A;  1N50 A;  1N15 A;  1DY7 A;  1H9X A;  1HZU A;  1H9Y A;  1AOM A;  1N90 A;  1BL9 A;  1HJ3 A;  1AOQ A;  1AOF A; 
#chains in the Genus database with same CATH topology
 2GBI A;  3VJL A;  3D4L A;  3OPM A;  1H4I A;  4N8D A;  4PNZ A;  1GQ1 A;  3KWJ A;  1QKS A;  3O9V A;  4AAH A;  3G0B A;  3SX4 A;  1R9N A;  1KV9 A;  5I7U A;  1W6S A;  1WCY A;  1N15 A;  4JH0 A;  2G63 A;  1H9X A;  2QTB A;  2BUA A;  2AJC A;  3WQH A;  2IIV A;  4MAE A;  2BGN A;  1AOM A;  2RGU A;  5T4E A;  4WJL A;  2BGR A;  5T4H A;  2OAG A;  5J3J A;  3Q0T A;  1HJ3 A;  4N8E A;  4DTC A;  3C45 A;  3SWW A;  1NU6 A;  1RWQ A;  3G0G A;  2OPH A;  1HCM A;  3VJK A;  4CVC A;  2AJ8 A;  1NNO A;  5KBY A;  3EIO A;  4QZV A;  2AJB A;  4PV7 A;  2ONC A;  1DY7 A;  2OQV A;  3QBJ A;  2FJP A;  2I3Z A;  3KWF A;  3O95 A;  2BUB A;  5T4B A;  2RIP A;  1H4J A;  1H9Y A;  1LRW A;  3OC0 A;  4KR0 A;  4G1F A;  3F8S A;  2QJR A;  4DSZ A;  3CCC A;  4A5S A;  1TK3 A;  4LKO A;  2G5P A;  2AD7 A;  1U8E A;  2JID A;  1HJ5 A;  2GBG A;  4DSA A;  3H0C A;  1ORV A;  4FFW A;  4J3J A;  1HZV A;  1E2R A;  1GJQ A;  3G0D A;  5ISM A;  1PFQ A;  1NIR A;  2QT9 A;  2DCM A;  2EEP A;  1N50 A;  3VJM A;  1TKR A;  2Z3W A;  1FLG A;  3C43 A;  4MH1 A;  1XFD A;  1N1M A;  2I78 A;  2D0V A;  4FFV A;  2Z3Z A;  3BJM A;  1AOQ A;  1AOF A;  1Z68 A;  2I03 A;  2P8S A;  4CVB A;  1HJ4 A;  2HHA A;  1ORW A;  2GBF A;  1KB0 A;  2GBC A;  2IIT A;  1X70 A;  2QOE A;  3HAB A;  2BUC A;  1NU8 A;  2OAE A;  2ECF A;  5LLS A;  3W2T A;  1R9M A;  2AD8 A;  5T4F A;  1HZU A;  3NOX A;  2OGZ A;  2OLE A;  1W1I A;  3HAC A;  4TQO A;  1N90 A;  3CCB A;  3G0C A;  4Q1V A;  2AJD A;  2D5L A;  1J2E A;  1BL9 A;  3Q8W A;  1YIQ A;  4L72 A;  1G72 A;  2AJL I;  2QKY A;  2OQI A;  2AD6 A;  2G5T A; 
#chains in the Genus database with same CATH homology
 1HJ5 A;  1HJ4 A;  1HZV A;  1E2R A;  1GQ1 A;  1GJQ A;  1NIR A;  1HCM A;  1QKS A;  1NNO A;  1N50 A;  1N15 A;  1DY7 A;  1H9X A;  1HZU A;  1H9Y A;  1AOM A;  1N90 A;  1BL9 A;  1HJ3 A;  1AOQ A;  1AOF A; 
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