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(-) Description

Title :  CRYSTAL STRUCTURE OF HIGH-MOLECULAR WEIGHT CYTOCHROME C FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F) IN THE PRESENCE OF ZINC ION
 
Authors :  N. Shibata, K. Suto, M. Sato, Y. Morimoto, M. Kitamura, Y. Higuchi
Date :  17 Jan 07  (Deposition) - 15 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome C3 Motifs, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Osuka, K. Suto, M. Sato, N. Shibata, M. Kitamura, Y. Morimoto, K. Ozawa, H. Akutsu, Y. Higuchi, N. Yasuoka
Structure Of High-Molecular Weight Cytochrome C From Desulfovibrio Vulgaris (Miyazaki F)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIGH-MOLECULAR-WEIGHT CYTOCHROME C
    Chains: A
    Organism Scientific: DESULFOVIBRIO VULGARIS STR. 'MIYAZAKI F'
    Organism Taxid: 883
    Strain: MIYAZAKI F

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric/Biological Unit (3, 24)
No.NameCountTypeFull Name
1HEM16Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA4Ligand/IonSODIUM ION
3ZN4Ligand/IonZINC ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:190 , LYS A:193 , GLU A:415 , ASP A:419 , GLU A:553BINDING SITE FOR RESIDUE ZN A 557
02AC2SOFTWAREHIS A:534 , GLU A:540 , GLU A:549BINDING SITE FOR RESIDUE ZN A 558
03AC3SOFTWARELYS A:355 , GLU A:442 , HEM A:1309BINDING SITE FOR RESIDUE ZN A 559
04AC4SOFTWAREHIS A:320 , LYS A:323 , ILE A:324 , ASP A:325 , HOH A:1361BINDING SITE FOR RESIDUE ZN A 560
05AC5SOFTWARELYS A:307 , LYS A:523 , HIS A:527 , HOH A:1409BINDING SITE FOR RESIDUE NA A 561
06AC6SOFTWARELYS A:32 , GLU A:124 , HOH A:1494BINDING SITE FOR RESIDUE NA A 562
07AC7SOFTWAREASP A:136 , HOH A:1513BINDING SITE FOR RESIDUE NA A 563
08AC8SOFTWAREMET A:279 , HEM A:1308 , HOH A:1319BINDING SITE FOR RESIDUE NA A 564
09AC9SOFTWAREILE A:48 , PHE A:64 , HIS A:66 , HIS A:69 , GLU A:82 , CYS A:83 , CYS A:86 , HIS A:87 , LEU A:97 , LYS A:98 , PHE A:99 , ARG A:101 , TYR A:114 , ARG A:221 , HIS A:225 , ILE A:229 , HEM A:1307 , HOH A:1428 , HOH A:1512BINDING SITE FOR RESIDUE HEM A 1301
10BC1SOFTWAREVAL A:62 , THR A:63 , PHE A:64 , ARG A:68 , HIS A:69 , VAL A:73 , PHE A:99 , ASN A:117 , CYS A:118 , CYS A:121 , HIS A:122 , GLN A:125 , LYS A:131 , THR A:132 , GLY A:133 , HOH A:1417 , HOH A:1469BINDING SITE FOR RESIDUE HEM A 1302
11BC2SOFTWAREILE A:48 , GLY A:49 , VAL A:50 , MET A:51 , LEU A:57 , GLU A:58 , LEU A:59 , VAL A:62 , LYS A:111 , TYR A:114 , HIS A:115 , CYS A:118 , ILE A:119 , GLN A:135 , ASP A:136 , GLU A:138 , CYS A:139 , CYS A:142 , HIS A:143BINDING SITE FOR RESIDUE HEM A 1303
12BC3SOFTWAREGLY A:156 , LEU A:157 , HIS A:162 , HIS A:165 , ASN A:180 , CYS A:181 , CYS A:184 , HIS A:185 , GLU A:202 , SER A:204 , LEU A:270 , GLU A:271 , THR A:315 , CYS A:316 , ARG A:317 , ILE A:324 , HEM A:1306 , HOH A:1333 , HOH A:1470 , HOH A:1477BINDING SITE FOR RESIDUE HEM A 1304
13BC4SOFTWARELYS A:94 , HIS A:185 , HIS A:186 , LEU A:195 , ASP A:203 , SER A:204 , CYS A:205 , CYS A:208 , HIS A:209 , LYS A:216 , PRO A:218 , ALA A:223 , GLN A:227 , HOH A:1476BINDING SITE FOR RESIDUE HEM A 1305
14BC5SOFTWARELEU A:161 , ARG A:164 , HIS A:165 , ILE A:171 , GLN A:227 , CYS A:228 , CYS A:231 , HIS A:232 , ASP A:243 , SER A:244 , GLY A:245 , PHE A:261 , HEM A:1304 , HOH A:1474BINDING SITE FOR RESIDUE HEM A 1306
15BC6SOFTWAREVAL A:46 , HIS A:66 , GLN A:154 , ILE A:155 , ARG A:206 , LEU A:220 , ARG A:221 , ALA A:224 , HIS A:225 , CYS A:228 , HIS A:232 , VAL A:247 , SER A:248 , CYS A:249 , CYS A:252 , HIS A:253 , HEM A:1301 , HOH A:1331 , HOH A:1503BINDING SITE FOR RESIDUE HEM A 1307
16BC7SOFTWAREARG A:272 , GLN A:274 , PHE A:304 , HIS A:306 , HIS A:309 , SER A:313 , THR A:315 , CYS A:316 , CYS A:319 , HIS A:320 , ASP A:325 , ASN A:326 , CYS A:327 , THR A:328 , NA A:564 , HOH A:1318 , HOH A:1364BINDING SITE FOR RESIDUE HEM A 1308
17BC8SOFTWARECYS A:319 , HIS A:320 , HIS A:321 , VAL A:322 , ASN A:326 , CYS A:327 , CYS A:330 , HIS A:331 , ASP A:338 , GLY A:339 , ASN A:340 , ALA A:347 , SER A:353 , LYS A:355 , GLU A:442 , ZN A:559 , HOH A:1452BINDING SITE FOR RESIDUE HEM A 1309
18BC9SOFTWAREVAL A:302 , PHE A:304 , ASN A:305 , HIS A:309 , MET A:354 , SER A:356 , CYS A:357 , CYS A:360 , HIS A:361 , ARG A:428 , LEU A:476 , THR A:479 , HEM A:1312BINDING SITE FOR RESIDUE HEM A 1310
19CC1SOFTWAREVAL A:365 , ALA A:369 , CYS A:370 , CYS A:373 , HIS A:374 , MET A:377 , THR A:379 , GLN A:384 , PRO A:385 , ILE A:471 , ASP A:474 , LEU A:476 , PHE A:480 , HIS A:481 , THR A:486 , VAL A:487 , ALA A:489 , GLY A:490 , HOH A:1385BINDING SITE FOR RESIDUE HEM A 1311
20CC2SOFTWAREVAL A:280 , LEU A:281 , PRO A:282 , GLY A:297 , ALA A:298 , MET A:299 , ILE A:344 , MET A:348 , HIS A:349 , CYS A:357 , HIS A:361 , GLN A:384 , ALA A:388 , CYS A:389 , CYS A:392 , HIS A:393 , HEM A:1310 , HOH A:1366BINDING SITE FOR RESIDUE HEM A 1312
21CC3SOFTWARETHR A:434 , LEU A:435 , ILE A:440 , ILE A:446 , LEU A:458 , HIS A:460 , VAL A:487 , CYS A:488 , CYS A:491 , HIS A:492 , PRO A:501 , LYS A:503 , CYS A:504 , TYR A:526 , HEM A:1315 , HOH A:1471 , HOH A:1503BINDING SITE FOR RESIDUE HEM A 1313
22CC4SOFTWAREPHE A:376 , LYS A:378 , CYS A:491 , HIS A:492 , HIS A:493 , ASN A:494 , PRO A:502 , LYS A:503 , CYS A:504 , CYS A:507 , HIS A:508 , ASP A:518 , PRO A:520 , ALA A:525 , GLN A:528 , GLN A:529 , HOH A:1328 , HOH A:1329BINDING SITE FOR RESIDUE HEM A 1314
23CC5SOFTWARELEU A:458 , LYS A:462 , ILE A:463 , THR A:466 , LEU A:467 , GLN A:529 , CYS A:530 , CYS A:533 , HIS A:534 , LEU A:539 , GLU A:549 , CYS A:550 , HEM A:1313 , HOH A:1380 , HOH A:1472BINDING SITE FOR RESIDUE HEM A 1315
24CC6SOFTWAREALA A:422 , ILE A:446 , GLY A:447 , VAL A:448 , LEU A:449 , SER A:450 , ASP A:451 , LYS A:452 , TYR A:453 , SER A:456 , LYS A:523 , TYR A:526 , HIS A:527 , CYS A:530 , MET A:531 , CYS A:547 , CYS A:550 , HIS A:551 , HOH A:1502BINDING SITE FOR RESIDUE HEM A 1316

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E84)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2E84)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E84)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E84)

(-) Exons   (0, 0)

(no "Exon" information available for 2E84)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:513
 aligned with Q8VUI3_DESVU | Q8VUI3 from UniProtKB/TrEMBL  Length:556

    Alignment length:524
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551    
         Q8VUI3_DESVU    32 KPLPGSTGEQRADLVEIGVMAKFGNLELPKVTFPHDRHSEAVAKVAAPGKECATCHKNDDKGKMSLKFMRLEDTTAADLKNIYHANCIGCHTEQAKAGKKTGPQDGECRSCHNPKPMASSWKQIGLDKSLHFRHVAAKAIAPVNDPQKNCGACHHVYDEAAKKLSWVKNKEDSCRACHGDARVEKKPSLREAAHTQCITCHRSVAAAPAKADSGPVSCAGCHDPAMQAKFKVVRDVPRLERGQPDAAMVLPVVGPGAKDTPKGMKGAMKPVAFNHKVHEAASNTCRACHHVKIDNCTTCHTLEGVKDGNFVQIEKAMHQPDSMKSCVGCHNQKVQAPACAGCHGFMKTGAKPQPEAACGVCHADPVGMDAKTVADGGLLKATKEQRADVAAATLAARRTTKGTLPADDIPEFVTIGVLSDKYEPSKLPHRKIVNTLMAAIGDDKLAGTFHTDKATVCAGCHHNSPASKTPPKCASCHGQPFDAAKGDRPGLKAAYHQQCMGCHNRMKLEKPADTACAECHKERA 555
               SCOP domains d2e84a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2e84A01 A:32-151 Cytochrome C3                                                                                          2e84A02 A:152-263 Cytochrome C3                                                                                 -----------2e84A03 A:275-4   31 Cytochrome C3                                                                                                                           2e84A04 A:432-555 Cytochrome C3                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..ee..eeeehhhhhhh......eeeehhhhhhhhhhhh............................hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh.....ee.......hhhhhhhhhh............hhhhh..ee......ee.......hhhhh..........hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.................eeee.........---.........eeeehhhhhhh.............hhhhh.....hhhhh..hhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhh.........hhhhhh......hhhhhhh......hhhhhhhhhhhhhhhh.......hhhhh...eee.........eeehhhhhhhhhhhhhh.hhhhhhhh...hhhhhhh...........hhhhh...-------...hhhhhhhhhhhhhhhhhh..-....hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e84 A  32 KPLPGSTGEQRADLVEIGVMAKFGNLELPKVTFPHDRHSEAVAKVAAPGKECATCHKNDDKGKMSLKFMRLEDTTAADLKNIYHANCIGCHTEQAKAGKKTGPQDGECRSCHNPKPMASSWKQIGLDKSLHFRHVAAKAIAPVNDPQKNCGACHHVYDEAAKKLSWVKNKEDSCRACHGDARVEKKPSLREAAHTQCITCHRSVAAAPAKADSGPVSCAGCHDPAMQAKFKVVRDVPRLERGQPDAAMVLPVVGPGAK---KGMKGAMKPVAFNHKVHEAASNTCRACHHVKIDNCTTCHTLEGVKDGNFVQIEKAMHQPDSMKSCVGCHNQKVQAPACAGCHGFMKTGAKPQPEAACGVCHADPVGMDAKTVADGGLLKATKEQRADVAAATLAARRTTKGTLPADDIPEFVTIGVLSDKYEPSKLPHRKIVNTLMAAIGDDKLAGTFHTDKATVCAGCHHNSPASKTPPKCASCHGQ-------DRPGLKAAYHQQCMGCHNRMKLE-PADTACAECHKERA 555
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       | - |     301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501        |-      |521       531        |-|      551    
                                                                                                                                                                                                                                                                                           289 293                                                                                                                                                                                                                      510     518                   540 |             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        542
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E84)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8VUI3_DESVU | Q8VUI3)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  2e84
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        Q8VUI3_DESVU | Q8VUI3: 1z1n

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