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(-) Description

Title :  CRYSTAL STRUCTURE OF COMPLEMENT FACTOR D MUTANT R202A AFTER ENSEMBLE REFINEMENT
 
Authors :  F. Forneris, B. T. Burnley, P. Gros
Date :  15 Oct 13  (Deposition) - 18 Dec 13  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B  (77x)
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Factor D, Ensemble Refinement (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Forneris, B. T. Burnley, P. Gros
Ensemble Refinement Shows Conformational Flexibility In Crystal Structures Of Human Complement Factor D
Acta Crystallogr. , Sect. D V. 70 733 2014
PubMed-ID: 24598742  |  Reference-DOI: 10.1107/S1399004713032549

(-) Compounds

Molecule 1 - COMPLEMENT FACTOR D
    ChainsA, B
    EC Number3.4.21.46
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System CommonHUMAN
    Expression System Taxid9606
    FragmentRESIDUES 26-253
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymADIPSIN, C3 CONVERTASE ACTIVATOR, PROPERDIN FACTOR D

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit (77x)AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:117 , PRO A:119 , VAL A:148 , LEU A:149 , ASP A:150 , ARG A:151 , MET A:169 , CYS A:170 , HOH A:1179BINDING SITE FOR RESIDUE GOL A1000
2AC2SOFTWAREVAL B:117 , PRO B:119 , VAL B:148 , LEU B:149 , ASP B:150 , ARG B:151 , MET B:169 , CYS B:170 , HOH B:1101 , HOH B:1103BINDING SITE FOR RESIDUE GOL B1000

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:26 -A:42
2A:123 -A:189
3A:154 -A:170
4A:179 -A:204
5B:26 -B:42
6B:123 -B:189
7B:154 -B:170
8B:179 -B:204

(-) Cis Peptide Bonds  (5, 361)

Asymmetric Unit
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 71, 72, 73, 74, 75, 76, 77Asp A:48 -Gly A:49
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77Gly A:200 -Ser A:201
31, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76Ala B:47 -Asp B:48
41, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77Gly B:200 -Ser B:201
51, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71, 72, 73, 74, 75, 76, 77Cys B:204 -Gly B:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034866V213GCFAD_HUMANDisease (CFDD)267606720A/BV188G
2UniProtVAR_034867C214RCFAD_HUMANDisease (CFDD)267606721A/BC189R
3UniProtVAR_034868I248MCFAD_HUMANPolymorphism2230216A/BI223M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034866V213GCFAD_HUMANDisease (CFDD)267606720AV188G
2UniProtVAR_034867C214RCFAD_HUMANDisease (CFDD)267606721AC189R
3UniProtVAR_034868I248MCFAD_HUMANPolymorphism2230216AI223M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034866V213GCFAD_HUMANDisease (CFDD)267606720BV188G
2UniProtVAR_034867C214RCFAD_HUMANDisease (CFDD)267606721BC189R
3UniProtVAR_034868I248MCFAD_HUMANPolymorphism2230216BI223M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CFAD_HUMAN26-253
 
  2A:1-228
B:1-228
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CFAD_HUMAN62-67
 
  2A:37-42
B:37-42
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CFAD_HUMAN202-213
 
  2A:177-188
B:177-188
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CFAD_HUMAN26-253
 
  1A:1-228
-
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CFAD_HUMAN62-67
 
  1A:37-42
-
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CFAD_HUMAN202-213
 
  1A:177-188
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CFAD_HUMAN26-253
 
  1-
B:1-228
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CFAD_HUMAN62-67
 
  1-
B:37-42
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CFAD_HUMAN202-213
 
  1-
B:177-188

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003277261ENSE00001231576chr19:859665-85974480CFAD_HUMAN1-19190--
1.2ENST000003277262ENSE00001231561chr19:860617-860773157CFAD_HUMAN19-71532A:1-46
B:1-46
46
46
1.3ENST000003277263ENSE00001231555chr19:860861-861005145CFAD_HUMAN71-119492A:46-94
B:46-94
49
49
1.4ENST000003277264ENSE00001374327chr19:861699-861956258CFAD_HUMAN120-205862A:95-180
B:95-180
86
86
1.5ENST000003277265ENSE00001354943chr19:863092-863606515CFAD_HUMAN206-253482A:181-228
B:181-228
48
48

(-) 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:228
 aligned with CFAD_HUMAN | P00746 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:228
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245        
           CFAD_HUMAN    26 ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLA 253
               SCOP domains d4cboa_ A: Factor D                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeee............eeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeeeeehhhhhh............eeeee.............eeee..eeeeee............eeeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GR---------------------------------M----- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:1-228 UniProt: 26-253                                                                                                                                                                                            PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ---------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:1-46 UniProt: 19-71          ------------------------------------------------Exon 1.4  PDB: A:95-180 UniProt: 120-205                                              Exon 1.5  PDB: A:181-228 UniProt: 206-253        Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:46-94 UniProt: 71-119           -------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 4cbo A   1 ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSAVCGNRKKPGIYTRVASYAAWIDSVLA 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        

Chain B from PDB  Type:PROTEIN  Length:228
 aligned with CFAD_HUMAN | P00746 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:228
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245        
           CFAD_HUMAN    26 ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLA 253
               SCOP domains d4cbob_ B: Factor D                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeee............eeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeeeeehhhhhh............eeee..............eeee..eeeeee.............eeeee...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GR---------------------------------M----- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:1-228 UniProt: 26-253                                                                                                                                                                                            PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ---------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: B:1-46 UniProt: 19-71          ------------------------------------------------Exon 1.4  PDB: B:95-180 UniProt: 120-205                                              Exon 1.5  PDB: B:181-228 UniProt: 206-253        Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: B:46-94 UniProt: 71-119           -------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 4cbo B   1 ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSAVCGNRKKPGIYTRVASYAAWIDSVLA 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CBO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CBO)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CFAD_HUMAN | P00746)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    GO:0006957    complement activation, alternative pathway    Any process involved in the activation of any of the steps of the alternative pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CFAD_HUMAN | P007461bio 1dfp 1dic 1dst 1dsu 1fdp 1hfd 2xw9 2xwa 2xwb 4cbn 4d9r 5fbe 5fbi 5fck 5mt0 5mt4 5nar 5naw 5nb6 5nb7 5nba 5tca 5tcc

(-) Related Entries Specified in the PDB File

4cbn CRYSTAL STRUCTURE OF COMPLEMENT FACTOR D MUTANT R202A AFTER CONVENTIONAL REFINEMENT