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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SIXTEEN HEME CYTOCHROME FROM DESULFOVIBRIO GIGAS
 
Authors :  T. Santos-Silva, J. M. Dias, M. J. Romao
Date :  04 Mar 05  (Deposition) - 04 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  X
Keywords :  Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Santos-Silva, J. M. Dias, M. J. Romao
Crystal Structure Of The Sixteen Heme Cytochrome From Desulfovibrio Gigas
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SIXTEEN HEME CYTOCHROME
    Chains: X
    Mutation: YES
    Organism Scientific: DESULFOVIBRIO GIGAS
    Organism Taxid: 879

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 26)

Asymmetric/Biological Unit (5, 26)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2HEC16Ligand/IonHEME C
3NAA1Ligand/IonN-ACETYL-D-ALLOSAMINE
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5ZN3Ligand/IonZINC ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR X:259 , ASN X:261 , NAA X:901 , HOH X:974 , HOH X:1138 , HOH X:1294BINDING SITE FOR RESIDUE NAG X 900
02AC2SOFTWARENAG X:900 , HOH X:1078BINDING SITE FOR RESIDUE NAA X 901
03AC3SOFTWAREHIS X:454 , HOH X:1034 , HOH X:1035 , HOH X:1036 , HOH X:1229 , HOH X:1264BINDING SITE FOR RESIDUE ZN X 701
04AC4SOFTWAREGLU X:387 , GLU X:390 , HOH X:1303 , HOH X:1304 , HOH X:1305BINDING SITE FOR RESIDUE ZN X 702
05AC5SOFTWAREMET X:421 , TRP X:428 , HEC X:616 , HOH X:1046 , HOH X:1311 , HOH X:1312BINDING SITE FOR RESIDUE ZN X 703
06AC6SOFTWAREILE X:16 , ILE X:18 , PHE X:34 , HIS X:36 , HIS X:39 , THR X:40 , LEU X:43 , CYS X:50 , CYS X:53 , HIS X:54 , PHE X:63 , LYS X:64 , PHE X:65 , ARG X:67 , TYR X:81 , ARG X:196 , HIS X:200 , VAL X:220 , LEU X:221 , HEC X:602 , HEC X:607 , HOH X:977BINDING SITE FOR RESIDUE HEC X 601
07AC7SOFTWAREPHE X:34 , LYS X:38 , HIS X:39 , LEU X:43 , CYS X:53 , PHE X:65 , CYS X:85 , CYS X:88 , HIS X:89 , TYR X:96 , PRO X:100 , ARG X:107 , HEC X:601 , HOH X:902 , HOH X:1098BINDING SITE FOR RESIDUE HEC X 602
08AC8SOFTWAREILE X:18 , ASP X:19 , THR X:20 , ALA X:21 , LEU X:27 , GLU X:28 , GLN X:29 , VAL X:32 , LYS X:74 , TYR X:81 , HIS X:82 , MET X:86 , ALA X:102 , GLU X:104 , CYS X:105 , CYS X:108 , HIS X:109 , PHE X:487 , GLN X:488 , HOH X:1067 , HOH X:1105BINDING SITE FOR RESIDUE HEC X 603
09AC9SOFTWARESER X:124 , LEU X:125 , HIS X:130 , HIS X:133 , SER X:148 , CYS X:149 , CYS X:152 , HIS X:153 , GLU X:170 , GLY X:171 , SER X:172 , CYS X:173 , ARG X:245 , ASN X:289 , CYS X:290 , VAL X:291 , HEC X:605 , HEC X:606 , HOH X:998 , HOH X:1012 , HOH X:1018BINDING SITE FOR RESIDUE HEC X 604
10BC1SOFTWARECYS X:152 , HIS X:154 , THR X:155 , TYR X:156 , CYS X:173 , CYS X:176 , HIS X:177 , SER X:184 , ARG X:190 , ALA X:198 , GLU X:201 , SER X:202 , HEC X:604 , HOH X:1026 , HOH X:1137 , HOH X:1232BINDING SITE FOR RESIDUE HEC X 605
11BC2SOFTWARELEU X:125 , ARG X:132 , HIS X:133 , ALA X:136 , CYS X:203 , CYS X:206 , HIS X:207 , GLU X:216 , GLY X:218 , PRO X:219 , TRP X:234 , LYS X:235 , HEC X:604 , HOH X:1232 , HOH X:1300BINDING SITE FOR RESIDUE HEC X 606
12BC3SOFTWAREVAL X:13 , ILE X:16 , HIS X:36 , LYS X:122 , PRO X:123 , THR X:195 , ARG X:196 , SER X:199 , HIS X:200 , CYS X:203 , HIS X:207 , PRO X:219 , VAL X:220 , LEU X:221 , CYS X:222 , CYS X:225 , HIS X:226 , HEC X:601 , HOH X:994 , HOH X:1108 , HOH X:1157 , HOH X:1288BINDING SITE FOR RESIDUE HEC X 607
13BC4SOFTWARELEU X:243 , ARG X:245 , GLN X:247 , PRO X:248 , THR X:251 , LEU X:253 , HIS X:280 , HIS X:283 , GLU X:284 , VAL X:287 , ASN X:289 , CYS X:290 , CYS X:293 , HIS X:294 , LEU X:303 , CYS X:306 , LYS X:386 , ARG X:389 , GOL X:804 , HOH X:1013 , HOH X:1147BINDING SITE FOR RESIDUE HEC X 608
14BC5SOFTWAREGLY X:94 , CYS X:293 , HIS X:294 , HIS X:295 , PRO X:296 , THR X:297 , GLN X:298 , SER X:302 , CYS X:306 , CYS X:310 , HIS X:311 , ASP X:318 , ASN X:320 , SER X:327 , GLN X:330 , THR X:335 , GOL X:805 , HOH X:1096BINDING SITE FOR RESIDUE HEC X 609
15BC6SOFTWAREVAL X:276 , PHE X:278 , ASP X:279 , HIS X:283 , PHE X:286 , VAL X:287 , THR X:292 , CYS X:293 , THR X:334 , CYS X:337 , CYS X:340 , HIS X:341 , GLN X:344 , ARG X:348 , SER X:449 , PRO X:450 , MET X:451 , HIS X:454 , PHE X:455 , HOH X:973 , HOH X:1011 , HOH X:1014 , HOH X:1196 , HOH X:1252 , HOH X:1264BINDING SITE FOR RESIDUE HEC X 610
16BC7SOFTWAREGLU X:350 , CYS X:351 , CYS X:354 , HIS X:355 , MET X:358 , SER X:364 , ASN X:366 , SER X:367 , SER X:449 , ALA X:452 , PHE X:455 , HIS X:456 , THR X:461 , MET X:462 , SER X:464 , GLY X:465 , HOH X:1040 , HOH X:1162 , HOH X:1211BINDING SITE FOR RESIDUE HEC X 611
17BC8SOFTWARELEU X:253 , VAL X:254 , ALA X:255 , ALA X:270 , PRO X:273 , VAL X:276 , THR X:313 , THR X:324 , ALA X:328 , HIS X:329 , CYS X:337 , LEU X:363 , SER X:364 , SER X:367 , CYS X:368 , CYS X:371 , HIS X:372 , PHE X:455 , GOL X:804 , HOH X:1052 , HOH X:1055BINDING SITE FOR RESIDUE HEC X 612
18BC9SOFTWAREVAL X:407 , VAL X:412 , PRO X:413 , LEU X:416 , TYR X:420 , PHE X:433 , HIS X:435 , ILE X:438 , TYR X:439 , CYS X:463 , CYS X:466 , HIS X:467 , LEU X:474 , PRO X:476 , LYS X:478 , CYS X:479 , HEC X:615 , HOH X:946 , HOH X:987 , HOH X:1304BINDING SITE FOR RESIDUE HEC X 613
19CC1SOFTWAREHIS X:468 , ASN X:469 , LYS X:478 , CYS X:479 , CYS X:482 , HIS X:483 , ASN X:493 , ALA X:500 , GLN X:504 , GOL X:803 , HOH X:945 , HOH X:1041 , HOH X:1087BINDING SITE FOR RESIDUE HEC X 614
20CC2SOFTWARELEU X:418 , PHE X:433 , PRO X:434 , LYS X:437 , ILE X:438 , LYS X:441 , GLN X:504 , CYS X:505 , CYS X:508 , HIS X:509 , PRO X:516 , HEC X:613 , HOH X:1016 , HOH X:1231BINDING SITE FOR RESIDUE HEC X 615
21CC3SOFTWARELEU X:418 , ASN X:419 , TYR X:420 , MET X:421 , ASP X:426 , GLU X:427 , TRP X:428 , LYS X:498 , HIS X:502 , ILE X:506 , HIS X:509 , LYS X:517 , ALA X:518 , CYS X:521 , CYS X:524 , HIS X:525 , ZN X:703 , HOH X:1046 , HOH X:1311 , HOH X:1312BINDING SITE FOR RESIDUE HEC X 616
22CC4SOFTWAREASP X:19 , HOH X:1306BINDING SITE FOR RESIDUE GOL X 801
23CC5SOFTWAREASN X:346 , LYS X:360 , GLU X:511 , HOH X:1307BINDING SITE FOR RESIDUE GOL X 802
24CC6SOFTWAREPRO X:357 , HIS X:468 , HEC X:614 , HOH X:1042 , HOH X:1154BINDING SITE FOR RESIDUE GOL X 803
25CC7SOFTWAREVAL X:254 , GLY X:256 , ARG X:389 , HEC X:608 , HEC X:612BINDING SITE FOR RESIDUE GOL X 804
26CC8SOFTWAREPRO X:296 , HEC X:609 , HOH X:1228BINDING SITE FOR RESIDUE GOL X 805

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z1N)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro X:185 -Val X:186
2Gly X:272 -Pro X:273
3Asn X:515 -Pro X:516

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z1N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z1N)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z1N)

(-) 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 X from PDB  Type:PROTEIN  Length:516
 aligned with T2G9Q2_DESGI | T2G9Q2 from UniProtKB/TrEMBL  Length:559

    Alignment length:520
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559
         T2G9Q2_DESGI    40 PKVDAIVIDTAAVFGKLEQPGVVFYHEKHTTALEKMAKDCTSCHVETEGKLSFKFARTVDPTSKNAMAEQYHANCMACHEKVVGSYPTAPQAAECKRCHVGPGVEGATVTPKPSLDLNLHGRHVVAEAKRLQVKEDESCKACHHTYDEAQKKLVYAKGEEGSCVYCHKQEPLPSPVQQDRVVPSTRDASHESCVNCHLSTRKAQTESGPVLCVGCHTAEAQAAWKKTAETPRLFRGQPDATLLVAGAATANGTVDVNWAAAGPGPVAFDHKAHEGFVGNCVTCHHPTQTGGSLAACGVACHTTTGSKDGNFVTTAQSAHQLGVTTSCVGCHTTQANARKECAGCHAPMQKTALSQNSCIQCHEAGFPTSGTQTLGKEEREATAAKILAAKDEKPKTVPLENVPEKLTLNYMDEKGDEWQAAEFPHRKIYQKLVEEAAKSPMANHFHGDALTMCSGCHHNAKPSLNPPKCASCHSKPFQERTANQPGLKGAFHNQCIGCHQEMQVNPKATDCQGCHKPKNS 559
               SCOP domains d1z1nx_ X: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1z1nX01 X:11-109 Cytochrome C3                                                                     -------1z1nX02 X:117-235 Cytochrome C3                                                                                        --------------------------------------------------------------------------------------------------1z1nX04 X:334-370,X:403-530          --------------------------------1z1nX04 X:334-370,X  :403-530 Cytochrome C3                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..hhhhhhh........eehhhhhhhhhhh..hhhhh..ee..ee...........hhhhhhhhhhhhhhhhhhh............hhhhhh.....hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhh..ee.hhhh.ee.......hhhhh..........--.....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.................eee...ee.....eeee........eeehhhhhhhhhh...........................hhhhh..hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..........hhhhh.........eeeehhhhhhhhhhhhhhhh.......hhhhh...eee...--.......eeehhhhhhhhhhhhhh.hhhhhhhhh...hhhhhh...........hhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhh......hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z1n X  11 PKVDAIVIDTAAVFGKLEQPGVVFYHEKHTTALEKMAKDCTSCHVETEGKLSFKFARTVDPTSKNAMAEQYHANCMACHEKVVGSYPTAPQAAECKRCHVGPGVEGATVTPKPSLDLNLHGRHVVAEAKRLQVKEDESCKACHHTYDEAQKKLVYAKGEEGSCVYCHKQEPLPSPV--DRVVPSTRDASHESCVNCHLSTRKAQTESGPVLCVGCHTAEAQAAWKKTAETPRLFRGQPDATLLVAGAATANGTVDVNWAAAGPGPVAFDHKAHEGFVGNCVTCHHPTQTGGSLAACGVACHTTTGSKDGNFVTTAQSAHQLGVTTSCVGCHTTQANARKECAGCHAPMQKTALSQNSCIQCHEAGFPTSGTQTLGKEEREATAAKILAAKDEKPKTVPLENVPEKLTLNYM--KGDEWQAAEFPHRKIYQKLVEEAAKSPMANHFHGDALTMCSGCHHNAKPSLNPPKCASCHSKPFQERTANQPGLKGAFHNQCIGCHQEMQVNPKATDCQGCHKPKNS 530
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     | 190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420|  |   430       440       450       460       470       480       490       500       510       520       530
                                                                                                                                                                                                         186  |                                                                                                                                                                                                                                     421  |                                                                                                          
                                                                                                                                                                                                            189                                                                                                                                                                                                                                        424
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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, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Z1N)

(-) Gene Ontology  (3, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (T2G9Q2_DESGI | T2G9Q2)
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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  Cis Peptide Bonds
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  1z1n
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 Related Entries

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        Q8VUI3_DESVU | Q8VUI3: 2e84

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