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(-) Description

Title :  FAB 4AB007 BOUND TO INTERLEUKIN-1-BETA
 
Authors :  W. Stark, V. Seibert
Date :  17 Jan 17  (Deposition) - 15 Feb 17  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,H,L,U,V
Biol. Unit 1:  H,L,U  (1x)
Biol. Unit 2:  A,B,V  (1x)
Keywords :  Interleukin-1-Beta, Fab 4Ab007, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Stark, V. Seibert
Structure Of A Novel, Fully Human Fab Binding To Interleuki 1-Beta.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FAB 4AB007 H-CHAIN
    Chains: H, A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB 4AB007 L-CHAIN
    Chains: L, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - INTERLEUKIN-1 BETA
    Chains: U, V
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: IL1B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABHLUV
Biological Unit 1 (1x):   HLU 
Biological Unit 2 (1x): AB   V

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY H:167 , HIS H:169 , THR H:188 , HOH H:426 , ASN L:137 , ASN L:138 , ASP L:167binding site for residue GOL H 301
2AC2SOFTWARELYS L:103 , ILE L:106 , GLU L:165 , GLN L:166 , HOH L:405 , HOH L:435 , HOH L:523binding site for residue GOL L 301
3AC3SOFTWARELYS B:169 , SER B:171 , GOL B:303 , PRO L:15 , PRO L:80 , HOH L:418binding site for residue GOL L 302
4AC4SOFTWARESER B:76 , HOH B:418 , ARG L:108 , ASP L:170 , HOH L:445 , HOH L:452binding site for residue GOL L 303
5AC5SOFTWARESER A:7 , ALA A:9 , GLN A:110 , GLY A:111 , THR A:112 , MET A:113binding site for residue GOL A 301
6AC6SOFTWAREPHE A:171 , PRO A:172 , SER A:182 , LEU A:183 , SER A:184 , GLN B:160 , SER B:162 , SER B:176 , SER B:177 , THR B:178 , HOH B:413binding site for residue GOL B 301
7AC7SOFTWARELYS B:103 , ILE B:106 , GLU B:165 , GLN B:166 , HOH B:409 , HOH B:450 , HOH B:510binding site for residue GOL B 302
8AC8SOFTWAREPRO B:15 , GLY B:16 , LEU B:78 , HOH B:429 , PRO L:15 , LYS L:169 , ASP L:170 , SER L:171 , GOL L:302binding site for residue GOL B 303
9AC9SOFTWARETYR A:52 , PRO A:53 , GLY A:54 , SER A:56 , ASP A:57 , SER A:132 , LYS A:134 , SER A:135 , THR A:136 , CYS A:221 , ASP V:54 , ILE V:56 , PRO V:57 , LYS V:103 , GLU V:105 , SER V:123 , THR V:124 , SER V:125 , PRO V:131 , VAL V:132 , LEU V:134 , ASP V:142binding site for Di-peptide LYS V 55 and SER A 133

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:145 -A:201
3B:23 -B:88
4B:134 -B:194
5H:22 -H:96
6H:145 -H:201
7H:221 -L:214
8L:23 -L:88
9L:134 -L:194

(-) Cis Peptide Bonds  (15, 15)

Asymmetric Unit
No.Residues
1Phe H:151 -Pro H:152
2Glu H:153 -Pro H:154
3Ser L:7 -Pro L:8
4Tyr L:140 -Pro L:141
5Tyr U:90 -Pro U:91
6Phe A:151 -Pro A:152
7Glu A:153 -Pro A:154
8Ser A:220 -Cys A:221
9Ser B:7 -Pro B:8
10Tyr B:140 -Pro B:141
11Glu V:37 -Gln V:38
12Asn V:53 -Asp V:54
13Lys V:74 -Asp V:75
14Tyr V:90 -Pro V:91
15Lys V:97 -Arg V:98

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MVZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MVZ)

(-) Exons   (0, 0)

(no "Exon" information available for 5MVZ)

(-) 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:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee........eeeeehhh.eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mvz A   1 EVQLVESGAEVKKPGESLKISCKGSGYTFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCARFVSLDAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC 221
                                    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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeee....eeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhh.eeeeeeee..eeee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mvz B   1 EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWLWTFGQGTKVEIKRSVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeeee....eeee........eeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mvz H   1 EVQLVESGAEVKKPGESLKISCKGSGYTFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCARFVSLDAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeee....eeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhh.eeeeeeee..eeee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mvz L   1 EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWLWTFGQGTKVEIKRSVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECE 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain U from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eee.....eee........eeeee........eeeeeeee..eeeeeeeeee..eeeeeeee...........hhhh.eeeeee..eeeeee.......ee......ee.ee......eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mvz U   3 VRSLNCTLRDSSLVMSGPYELKALHLEQQVVFSMSFVQGEESNDKIPVALGLKEKNLYLSCVLKDDKPTLQLESVDPKNYPKKKMEKRFVFNKIEINNKLEFESAQFPNWYISTSQAENMPVFLGDITDFTMQFVS 152
                                    12||      25     || 40        50        60        70        80        90       100       110       120       130    || 146      
                                     13|            31|                                                                                               135|          
                                      17             37                                                                                                142          


Chain V from PDB  Type:PROTEIN  Length:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....eeee.....eeee........eeeee............ee....eeeeeee....eeeeeee...........................ee.......eeeee....ee.eee......ee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mvz V   3 VRSLNCTLRDSQQKSLVMSGPYELKALHLMEQQVVFSMSFVQGSNDKIPVALGLKEKNLYLSCVLKDDKPTLQLESVDPKNYPKKKMEKRFVFNKIEINNKLEFESAQFPNWYISTSQAENMPVFLGGTKGGQDITDFTMQFVS 152
                                    12        22        36        46  ||    58        68        78        88        98       108       118       128       138       148    
                                                       31|           49|                                                                                                    
                                                        36            52
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 5MVZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MVZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MVZ)

(-) Gene Ontology  (146, 152)

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  5mvz
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 Related Entries

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

UniProtKB/Swiss-Prot
        IL1B_HUMAN | P01584: 1hib 1i1b 1iob 1itb 1l2h 1s0l 1t4q 1too 1tp0 1twe 1twm 21bi 2i1b 2kh2 2nvh 31bi 3ltq 3o4o 3pok 41bi 4dep 4g6j 4g6m 4gaf 4gai 4i1b 5bvp 5i1b 6i1b 7i1b 9ilb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5MVZ)