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(-) Description

Title :  THE CRYSTAL STRUCTURE OF FLAVOHEMOGLOBIN FROM R. EUTROPHUS IN COMPLEX WITH ECONAZOLE
 
Authors :  E. El Hammi, E. Warkentin, U. Demmer, U. Ermler, L. Baciou
Date :  27 Sep 10  (Deposition) - 16 Mar 11  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Globin Fold, Antiparallel Beta-Barrel, Alpha/Beta Fold, Hem-, Fad-, Nad- Binding Domains, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. El Hammi, E. Warkentin, U. Demmer, F. Limam, N. M. Marzouki, U. Ermler, L. Baciou
Structure Of Ralstonia Eutropha Flavohemoglobin In Complex With Three Antibiotic Azole Compounds.
Biochemistry V. 50 1255 2011
PubMed-ID: 21210640  |  Reference-DOI: 10.1021/BI101650Q

(-) Compounds

Molecule 1 - FLAVOHEMOGLOBIN
    ChainsB, A
    EC Number1.14.12.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    GeneHMP, FHP, PHG200
    Organism CommonCUPRIAVIDUS NECATOR
    Organism ScientificRALSTONIA EUTROPHA
    Organism Taxid381666
    StrainH16
    SynonymHEMOGLOBIN-LIKE PROTEIN, FLAVOHEMOGLOBIN, FHP, NITRIC OXIDE DIOXYGENASE, NO OXYGENASE, NOD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1DGG2Ligand/Ion1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL
2ECN2Ligand/Ion1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (5, 5)
No.NameCountTypeFull Name
1DGG1Ligand/Ion1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL
2ECN1Ligand/Ion1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1DGG1Ligand/Ion1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL
2ECN1Ligand/Ion1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 3 (5, 5)
No.NameCountTypeFull Name
1DGG1Ligand/Ion1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL
2ECN1Ligand/Ion1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5PO41Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL B:42 , PHE B:43 , ASN B:44 , ILE B:81 , LYS B:84 , HIS B:85 , LEU B:88 , VAL B:90 , GLN B:94 , TYR B:95 , TYR B:126 , LEU B:129 , ALA B:130 , PRO B:398 , ASP B:399 , DGG B:406 , ECN B:411 , HOH B:429BINDING SITE FOR RESIDUE HEM B 404
2AC2SOFTWAREASN B:44 , ALA B:46 , GLU B:49 , GLN B:50 , LYS B:84 , TYR B:190 , ARG B:206 , GLN B:207 , TYR B:208 , SER B:209 , SER B:222 , VAL B:223 , LYS B:224 , GLN B:231 , PRO B:232 , GLY B:234 , TYR B:235 , VAL B:236 , SER B:237 , VAL B:276 , THR B:279 , GLU B:394 , VAL B:395 , PHE B:396 , HOH B:409 , HOH B:415 , HOH B:423 , HOH B:452BINDING SITE FOR RESIDUE FAD B 405
3AC3SOFTWAREALA B:60 , ALA B:63 , GLU B:66 , VAL B:77 , ILE B:81 , TYR B:126 , LEU B:129 , GLU B:403 , HEM B:404 , ECN B:411BINDING SITE FOR RESIDUE DGG B 406
4AC4SOFTWAREPHE A:43 , ASN A:44 , HIS A:47 , ILE A:81 , LYS A:84 , HIS A:85 , LEU A:88 , VAL A:90 , GLN A:94 , TYR A:95 , VAL A:98 , TYR A:126 , ALA A:130 , PRO A:398 , ECN A:411BINDING SITE FOR RESIDUE HEM A 404
5AC5SOFTWAREASN A:44 , ALA A:46 , GLN A:48 , GLU A:49 , TYR A:190 , ARG A:206 , GLN A:207 , TYR A:208 , SER A:209 , SER A:222 , VAL A:223 , LYS A:224 , GLU A:226 , GLN A:231 , PRO A:232 , GLY A:234 , TYR A:235 , VAL A:236 , SER A:237 , VAL A:276 , THR A:279 , VAL A:395 , PHE A:396 , GLY A:397 , PRO B:15 , TYR B:62BINDING SITE FOR RESIDUE FAD A 405
6AC6SOFTWAREALA A:63 , ASN A:67 , LEU A:74 , VAL A:77 , ECN A:411BINDING SITE FOR RESIDUE DGG A 406
7AC7SOFTWAREMET A:310 , ARG A:311 , ASP A:312 , ARG A:313BINDING SITE FOR RESIDUE PO4 A 407
8AC8SOFTWAREILE B:24 , ILE B:25 , PHE B:28 , PHE B:43 , GLN B:53 , ALA B:56 , LEU B:57 , LEU B:102 , HEM B:404 , DGG B:406BINDING SITE FOR RESIDUE ECN B 411
9AC9SOFTWAREILE A:24 , PHE A:43 , GLN A:53 , ALA A:56 , LEU A:57 , LEU A:102 , ILE A:106 , HEM A:404 , DGG A:406BINDING SITE FOR RESIDUE ECN A 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OZV)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Gly B:51 -Gln B:52
2Ala B:291 -Pro B:292
3Arg B:294 -Gln B:295
4Gln A:48 -Glu A:49
5Pro A:292 -Pro A:293
6Pro A:293 -Arg A:294
7Asp A:399 -Leu A:400

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OZV)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HMP_CUPNH9-133
 
  2A:9-133
B:9-133
2FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.HMP_CUPNH152-262
 
  2A:152-262
B:152-262
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HMP_CUPNH9-133
 
  1A:9-133
-
2FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.HMP_CUPNH152-262
 
  1A:152-262
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HMP_CUPNH9-133
 
  1-
B:9-133
2FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.HMP_CUPNH152-262
 
  1-
B:152-262
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HMP_CUPNH9-133
 
  2A:9-133
B:9-133
2FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.HMP_CUPNH152-262
 
  2A:152-262
B:152-262

(-) Exons   (0, 0)

(no "Exon" information available for 3OZV)

(-) Sequences/Alignments

Asymmetric 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:403
 aligned with HMP_CUPNH | P39662 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:403
                                    10        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   
            HMP_CUPNH     1 MLTQKTKDIVKATAPVLAEHGYDIIKCFYQRMFEAHPELKNVFNMAHQEQGQQQQALARAVYAYAENIEDPNSLMAVLKNIANKHASLGVKPEQYPIVGEHLLAAIKEVLGNAATDDIISAWAQAYGNLADVLMGMESELYERSAEQPGGWKGWRTFVIREKRPESDVITSFILEPADGGPVVNFEPGQYTSVAIDVPALGLQQIRQYSLSDMPNGRSYRISVKREGGGPQPPGYVSNLLHDHVNVGDQVKLAAPYGSFHIDVDAKTPIVLISGGVGLTPMVSMLKVALQAPPRQVVFVHGARNSAVHAMRDRLREAAKTYENLDLFVFYDQPLPEDVQGRDYDYPGLVDVKQIEKSILLPDADYYICGPIPFMRMQHDALKNLGIHEARIHYEVFGPDLFAE 403
               SCOP domains d3ozva1 A:1-150 automated matches                                                                                                                     d3ozva2 A:151-261 automated matches                                                                            d3ozva3 A:262-403 automated matches                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee....eeeeeeee.............eeeeeeee....eeeeeeee.........eeeeee..........hhhhhhhhhh....eeee................eeeeee...hhhhhhhhhhhh......eeeeeee.......hhhhhhhhhhhh..eeeeeee..............ee...hhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.hhh.eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------GLOBIN  PDB: A:9-133 UniProt: 9-133                                                                                          ------------------FAD_FR  PDB: A:152-262 UniProt: 152-262                                                                        --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ozv A   1 MLTQKTKDIVKATAPVLAEHGYDIIKCFYQRMFEAHPELKNVFNMAHQEQGQQQQALARAVYAYAENIEDPNSLMAVLKNIANKHASLGVKPEQYPIVGEHLLAAIKEVLGNAATDDIISAWAQAYGNLADVLMGMESELYERSAEQPGGWKGWRTFVIREKRPESDVITSFILEPADGGPVVNFEPGQYTSVAIDVPALGLQQIRQYSLSDMPNGRSYRISVKREGGGPQPPGYVSNLLHDHVNVGDQVKLAAPYGSFHIDVDAKTPIVLISGGVGLTPMVSMLKVALQAPPRQVVFVHGARNSAVHAMRDRLREAAKTYENLDLFVFYDQPLPEDVQGRDYDYPGLVDVKQIEKSILLPDADYYICGPIPFMRMQHDALKNLGIHEARIHYEVFGPDLFAE 403
                                    10        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   

Chain B from PDB  Type:PROTEIN  Length:403
 aligned with HMP_CUPNH | P39662 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:403
                                    10        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   
            HMP_CUPNH     1 MLTQKTKDIVKATAPVLAEHGYDIIKCFYQRMFEAHPELKNVFNMAHQEQGQQQQALARAVYAYAENIEDPNSLMAVLKNIANKHASLGVKPEQYPIVGEHLLAAIKEVLGNAATDDIISAWAQAYGNLADVLMGMESELYERSAEQPGGWKGWRTFVIREKRPESDVITSFILEPADGGPVVNFEPGQYTSVAIDVPALGLQQIRQYSLSDMPNGRSYRISVKREGGGPQPPGYVSNLLHDHVNVGDQVKLAAPYGSFHIDVDAKTPIVLISGGVGLTPMVSMLKVALQAPPRQVVFVHGARNSAVHAMRDRLREAAKTYENLDLFVFYDQPLPEDVQGRDYDYPGLVDVKQIEKSILLPDADYYICGPIPFMRMQHDALKNLGIHEARIHYEVFGPDLFAE 403
               SCOP domains d3ozvb1 B:1-150 automated matches                                                                                                                     d3ozvb2 B:151-261 automated matches                                                                            d3ozvb3 B:262-403 automated matches                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Globin-3ozvB03 B:6-103                                                                            ----------------------------------------------------FAD_binding_6-3ozvB01 B:156-261                                                                           ---------NAD_binding_1-3ozvB05 B:271-379                                                                              ------------------------ Pfam domains (1)
           Pfam domains (2) -----Globin-3ozvB04 B:6-103                                                                            ----------------------------------------------------FAD_binding_6-3ozvB02 B:156-261                                                                           ---------NAD_binding_1-3ozvB06 B:271-379                                                                              ------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee....eeeeeeee.............eeeeeee......eeeeeee.........eeeeee.........hhhhhhhhhhh....eeee................eeeeee...hhhhhhhhhhhh......eeeeeee.........hhhhhh......eeeeeee..............ee.......hhhhhh....eeeee.hhhhhhhhhhhhhh...hhh.eee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------GLOBIN  PDB: B:9-133 UniProt: 9-133                                                                                          ------------------FAD_FR  PDB: B:152-262 UniProt: 152-262                                                                        --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ozv B   1 MLTQKTKDIVKATAPVLAEHGYDIIKCFYQRMFEAHPELKNVFNMAHQEQGQQQQALARAVYAYAENIEDPNSLMAVLKNIANKHASLGVKPEQYPIVGEHLLAAIKEVLGNAATDDIISAWAQAYGNLADVLMGMESELYERSAEQPGGWKGWRTFVIREKRPESDVITSFILEPADGGPVVNFEPGQYTSVAIDVPALGLQQIRQYSLSDMPNGRSYRISVKREGGGPQPPGYVSNLLHDHVNVGDQVKLAAPYGSFHIDVDAKTPIVLISGGVGLTPMVSMLKVALQAPPRQVVFVHGARNSAVHAMRDRLREAAKTYENLDLFVFYDQPLPEDVQGRDYDYPGLVDVKQIEKSILLPDADYYICGPIPFMRMQHDALKNLGIHEARIHYEVFGPDLFAE 403
                                    10        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   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OZV)

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HMP_CUPNH | P39662)
molecular function
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    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.
    GO:0008941    nitric oxide dioxygenase activity    Catalysis of the reaction: 2 NO + 2 O2 + NADPH + H+ = 2 nitrate + NADP+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0051409    response to nitrosative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  HMP_CUPNH | P39662
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HMP_CUPNH | P396621cqx 3ozu 3ozw

(-) Related Entries Specified in the PDB File

3ozu 3ozw