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(-) Description

Title :  MATURE OXY-COPE CATALYTIC ANTIBODY WITH HAPTEN
 
Authors :  E. C. Mundorff, H. D. Ulrich, R. C. Stevens
Date :  20 Oct 97  (Deposition) - 04 Feb 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Oxy-Cope, Catalytic Antibody, Fab Fragment (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. D. Ulrich, E. Mundorff, B. D. Santarsiero, E. M. Driggers, R. C. Stevens, P. G. Schultz
The Interplay Between Binding Energy And Catalysis In The Evolution Of A Catalytic Antibody.
Nature V. 389 271 1997
PubMed-ID: 9305839  |  Reference-DOI: 10.1038/38470
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OXY-COPE CATALYTIC ANTIBODY
    Cell: B LYMPHOCYTE
    Cell Line: AZ-28 HYBRIDOMA
    Chains: L, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: PERIPLASM
    Expression System Plasmid: PAZ-28
    Expression System Strain: 25F2
    Expression System Taxid: 562
    Expression System Vector: PAZ-28
    Expression System Vector Type: PLASMID
    Fragment: FAB FRAGMENT
    Fragment (source): CHAIN L, A, 108 - 211, CHAIN H, B, 114 - 214
    Organ: SPLEEN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CHIMERIC FAB FRAGMENT
    Other Details - Source: THE PROTEIN WAS PRODUCED AS CHIMERIC FAB FRAGMENT. THE CONSTANT DOMAINS ARE HUMAN, THE VARIABLE DOMAINS ARE MURINE. PRODUCTION BY EXPRESSION FROM PHOA PROMOTER
    Strain: SWISS WEBSTER
 
Molecule 2 - OXY-COPE CATALYTIC ANTIBODY
    Cell: B LYMPHOCYTE
    Cell Line: AZ-28 HYBRIDOMA
    Chains: H, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: PERIPLASM
    Expression System Plasmid: PAZ-28
    Expression System Strain: 25F2
    Expression System Taxid: 562
    Expression System Vector: PAZ-28
    Expression System Vector Type: PLASMID
    Fragment: FAB FRAGMENT
    Fragment (source): CHAIN L, A, 108 - 211, CHAIN H, B, 114 - 214
    Organ: SPLEEN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CHIMERIC FAB FRAGMENT
    Other Details - Source: THE PROTEIN WAS PRODUCED AS CHIMERIC FAB FRAGMENT. THE CONSTANT DOMAINS ARE HUMAN, THE VARIABLE DOMAINS ARE MURINE. PRODUCTION BY EXPRESSION FROM PHOA PROMOTER
    Strain: SWISS WEBSTER

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x):   HL
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CD8Ligand/IonCADMIUM ION
2HOP2Ligand/Ion(1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2HOP1Ligand/Ion(1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2HOP1Ligand/Ion(1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:198 , LEU A:201BINDING SITE FOR RESIDUE CD A 212
02AC2SOFTWAREASP L:167BINDING SITE FOR RESIDUE CD L 212
03AC3SOFTWARETYR A:49 , ASP A:56 , SER B:84 , GLU B:85BINDING SITE FOR RESIDUE CD A 213
04AC4SOFTWARESER H:74 , HOH H:1028BINDING SITE FOR RESIDUE CD H 1004
05AC5SOFTWAREGLN L:27 , GLU L:93 , HOH L:250BINDING SITE FOR RESIDUE CD L 213
06AC6SOFTWAREGLU L:143 , HOH L:229BINDING SITE FOR RESIDUE CD L 214
07AC7SOFTWAREASN H:199 , LYS H:206 , ASP H:208BINDING SITE FOR RESIDUE CD H 1005
08AC8SOFTWAREGLU A:143BINDING SITE FOR RESIDUE CD A 214
09AC9SOFTWAREGLU H:35 , GLY H:95 , HIS H:96 , ASP H:101 , TRP H:103 , TYR H:1001 , HOH H:1013 , LEU L:89 , TYR L:91 , TYR L:96BINDING SITE FOR RESIDUE HOP H 1006
10BC1SOFTWARELEU A:89 , TYR A:91 , HOH A:227 , HOH A:234 , GLU B:35 , HIS B:96 , ASP B:101 , TRP B:103 , TYR B:1001BINDING SITE FOR RESIDUE HOP B 1004
11CATUNKNOWNTRP H:47 , TRP H:103 , PHE L:36 , LEU L:89 , PHE L:98 , ALA H:93 , GLU H:35 , HIS H:96 , TYR L:91 , GLU H:50 , TYR L:96 , TYR H:1001 , ASN L:34 , ASP H:101HAPTEN BINDING SITE.

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Phe L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:146 -Pro H:147
5Ser A:7 -Pro A:8
6Phe A:94 -Pro A:95
7Tyr A:140 -Pro A:141
8Phe B:146 -Pro B:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1AXS)

(-) 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:211
 aligned with Q7Z3Y4_HUMAN | Q7Z3Y4 from UniProtKB/TrEMBL  Length:236

    Alignment length:211
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
        Q7Z3Y4_HUMAN     23 DIQMTQSPSSLSASVGDTVTITCRASQDISNYLAWFQQKPGKAPKSLIYGASSLQSGVQSKFSGSGSGTDFTLTISSLQPEDFATYYCQQYKSYPVTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  233
               SCOP domains d1axsa1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1axsa2 A:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1axsA01 A:1-108 Immunoglobulins                                                                             1axsA02 A:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee........eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee.......eeeee....hhh...eeeeeeeee.......eeeeee........eeeee...........eeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1axs A    1 ELVLTQSPSSMYASLGERVTITCKASQDINSYLNWFQQKPGKSPKTLIYRTNRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPYTFGSGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 


Chain B from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains d1axsb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1axsb2 B:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1axsB01 B:1-113 Immunoglobulins                                                                                         1axsB02 B:114-213 Immunoglobulins                                                                   - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..........eeeeee.....hhh.eeeeeeee...eeeeeeeee....eeee.hhh...eeeeee....eeeeee....hhh.eeeeeee...............eee..........eeeee..........eeeeeeeee...................eee............eeeeeeee........eeeeeeehhh.eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1axs B    1 QVQLLESGAELMKPGASVKISCKATGYTFSSFWIEWVKQRPGHGLEWIGEILPGSGGTHYNEKFKGKATFTADKSSNTAYMQLSSLTSEDSAVYYCARGHSYYFYDGDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50 |||    59        69        79  || || 86        96   || |103       113       123       133       143       153       163       173       183       193       203       213 
                                                                              52||                           82| ||              100| ||                                                                                                                 
                                                                              521|                           821 ||              1001 ||                                                                                                                 
                                                                                53                             823|                1003|                                                                                                                 
                                                                                                                 83                  101                                                                                                                 


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains d1axsh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1axsh2 H:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1axsH01 H:1-113 Immunoglobulins                                                                                         1axsH02 H:114-213 Immunoglobulins                                                                   - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee.....eeeeee.....hhh.eeeeeeee...eeeeeeeee....eeee.hhh...eeeeee....eeeeee....hhh.eeeeeee...............eeeee........eeeee..........eeeeeeeee...................eee............eeeeeeee........eeeeeeehhh.eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1axs H    1 QVQLLESGAELMKPGASVKISCKATGYTFSSFWIEWVKQRPGHGLEWIGEILPGSGGTHYNEKFKGKATFTADKSSNTAYMQLSSLTSEDSAVYYCARGHSYYFYDGDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50 |||    59        69        79  || || 86        96   || |103       113       123       133       143       153       163       173       183       193       203       213 
                                                                              52||                           82| ||              100| ||                                                                                                                 
                                                                              521|                           821 ||              1001 ||                                                                                                                 
                                                                                53                             823|                1003|                                                                                                                 
                                                                                                                 83                  101                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:211
 aligned with Q7Z3Y4_HUMAN | Q7Z3Y4 from UniProtKB/TrEMBL  Length:236

    Alignment length:211
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
        Q7Z3Y4_HUMAN     23 DIQMTQSPSSLSASVGDTVTITCRASQDISNYLAWFQQKPGKAPKSLIYGASSLQSGVQSKFSGSGSGTDFTLTISSLQPEDFATYYCQQYKSYPVTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  233
               SCOP domains d1axsl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1axsl2 L:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1axsL01 L:1-108 Immunoglobulins                                                                             1axsL02 L:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee........eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee.......eeeee...........eeeeeeee.......eeeeee........eeeee...........eeeeeee.hhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1axs L    1 ELVLTQSPSSMYASLGERVTITCKASQDINSYLNWFQQKPGKSPKTLIYRTNRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPYTFGSGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (4, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (homo sapiens) (4)
1a1axsA02A:109-211
1b1axsB02B:114-213
1c1axsH02H:114-213
1d1axsL02L:109-211
1e1axsB01B:1-113
1f1axsH01H:1-113
1g1axsA01A:1-108
1h1axsL01L:1-108

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,L   (Q7Z3Y4_HUMAN | Q7Z3Y4)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IGHG1_HUMAN | P01857: 1aj7 1aqk 1bey 1d5b 1d5i 1d6v 1dfb 1dn2 1e4k 1fc1 1fc2 1fcc 1gaf 1h3t 1h3u 1h3v 1h3w 1h3x 1h3y 1hkl 1hzh 1i7z 1l6x 1n7m 1op3 1oqo 1oqx 1pg7 1t83 1t89 1vge 2dts 2gj7 2i5y 2iwg 2j6e 2jb5 2jb6 2o5x 2o5y 2o5z 2osl 2qad 2ql1 2qqk 2qql 2qqn 2qr0 2r56 2rcj 2rcs 2vxq 2wah 3agv 3ave 3ay4 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3c2s 3cfj 3cfk 3csy 3d0l 3d0v 3d6g 3d85 3dj9 3dnk 3do3 3dro 3drq 3dvg 3dvn 3eyf 3eyo 3eyq 3fjt 3mcl 3o11 3ry6 3s7g 3sgj 3sgk 3tv3 3twc 3tyg 3u0w 3u7w 3u7y 3v7m 3v8c 3v95 3wjj 3wjl 3wkn 3wn5 4acp 4b7i 4bm7 4bsv 4bsw 4byh 4cdh 4d9q 4d9r 4dag 4dz8 4eow 4hix 4j12 4ku1 4lld 4llm 4llq 4n0u 4nqs 4nqt 4nqu 4nwt 4nwu 4o4y 4o51 4q6y 4q74 4q7d 4w4n 4w4o 4wi2 4wi3 4wi4 4wi5 4wi6 4wi7 4wi8 4wi9 4x4m 4x98 4x99 4xmp 4xny 4xnz 4xxd 4zne 5bw7 5c7k 5d4q 5d6d 5di8 5dj0 5dj2 5dj6 5dj8 5dja 5djc 5djd 5djx 5djy 5djz 5dk0 5dk2 5dvk 5dvl 5dvm 5dvn 5dvo 5gsq 5hsf 5hy9 5hye 5hyf 5hyi 5iq7 5iq9 5iw3 5iw6 5jih 5jii 5jik 5k33 5k8d 5kwg 5m3v 5v43 5v4e
UniProtKB/TrEMBL
        Q7Z3Y4_HUMAN | Q7Z3Y4: 1l7i 1pg7 1s78 2jix 4ogx 4ogy 4pub

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AXS)