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(-) Description

Title :  LINGO-1/LI81 FAB COMPLEX
 
Authors :  R. B. Pepinsky, J. W. Arndt, C. Quan, Y. Gao, O. Quintero-Monzon, X. Lee,
Date :  10 Feb 14  (Deposition) - 14 May 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.23
Chains :  Asym. Unit :  A,H,L
Biol. Unit 1:  A,H,L  (2x)
Biol. Unit 2:  A (1x),H (1x),L (1x)
Keywords :  Leucine Rich Repeat, Ig Domain, Membrane Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. B. Pepinsky, J. W. Arndt, C. Quan, Y. Gao, O. Quintero-Monzon, X. Lee S. Mi
Structure Of The Lingo-1-Anti-Lingo-1 Li81 Antibody Complex Provides Insights Into The Biology Of Lingo-1 And The Mechanism Of Action Of The Antibody Therapy.
J. Pharmacol. Exp. Ther. V. 350 110 2014
PubMed-ID: 24756303  |  Reference-DOI: 10.1124/JPET.113.211771

(-) Compounds

Molecule 1 - LEUCINE-RICH REPEAT AND IMMUNOGLOBULIN-LIKE DOMAIN- CONTAINING NOGO RECEPTOR-INTERACTING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Fragment: UNP RESIDUES 40-517
    Gene: LINGO1, LERN1, LRRN6A, UNQ201/PRO227
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LEUCINE-RICH REPEAT AND IMMUNOGLOBULIN DOMAIN-CONTAINING PROTEIN 1, LEUCINE-RICH REPEAT NEURONAL PROTEIN 1, LEUCINE-RICH REPEAT NEURONAL PROTEIN 6A
 
Molecule 2 - LIGHT CHAIN OF LI81 FAB, KAPPA 3
    Chains: L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - HEAVY CHAIN OF LI81 FAB, VH3-23
    Chains: H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : AHL
Biological Unit 1 (2x): AHL
Biological Unit 2 (1x): A (1x)H (1x)L (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 30)
No.NameCountTypeFull Name
1BMA6Ligand/IonBETA-D-MANNOSE
2NAG24Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 15)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:80 , ASN A:81 , ASN A:105BINDING SITE FOR MONO-SACCHARIDE NAG A 506 BOUND TO ASN A 105
2AC2SOFTWAREARG A:91 , ASN A:163 , ASN A:187BINDING SITE FOR MONO-SACCHARIDE NAG A 510 BOUND TO ASN A 163
3AC3SOFTWARELYS A:203 , ASN A:225 , TYR A:249 , GLY A:400BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 225 RESIDUES 513 TO 515
4AC4SOFTWAREARG A:6 , ARG A:22 , VAL A:24 , PRO A:211 , TYR A:212 , ASN A:235 , THR A:237BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 235 RESIDUES 507 TO 509
5AC5SOFTWARETHR A:232 , HIS A:233 , PHE A:252 , ASN A:254 , TYR A:257 , GLN A:278 , SER H:192 , THR H:196BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 254 RESIDUES 501 TO 503
6AC6SOFTWAREGLN A:278 , VAL A:280 , ASN A:302 , GLN A:353 , SER H:193 , GLN H:197BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 302 RESIDUES 504 TO 505
7AC7SOFTWAREGLN A:394 , ASN A:453 , GLY A:454 , THR A:455 , LEU A:473 , HIS A:474BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 453 RESIDUES 511 TO 512

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:3 -A:9
2A:7 -A:18
3A:334 -A:357
4A:336 -A:382
5A:407 -A:458
6H:22 -H:96
7H:145 -H:201
8L:23 -L:88
9L:135 -L:195

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Thr A:359 -Pro A:360
2Asp A:412 -Pro A:413
3Ser L:7 -Pro L:8
4Trp L:94 -Pro L:95
5Tyr L:141 -Pro L:142
6Phe H:151 -Pro H:152
7Glu H:153 -Pro H:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OQT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OQT)

(-) Exons   (0, 0)

(no "Exon" information available for 4OQT)

(-) 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:475
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee....eee..................eee.......ee............eee.......ee............eee...............................ee............eeee......ee............eeeee.......hhhhhh......eeeee.....ee............eeeee......ee...........eeeee.......hhhhhh......eee.......ee............eee.......ee............eee.........hhhhh.hhhhh.eee.....ee.hhhhhhhhhhhhhh........eeehhhhh..hhhhh...........eeeee.....eeeeee....eee...eeee......ee.....ee.......eee.....eee...hhhhheeeeee........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqt A   3 CPPRCECSAQDRAVLCHRKRFVAVPEGIPTETRLLDLGKNRIKTLNQDEFASFPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLTKLDISENKIVILLDYMFQDLYNLKSLEVGDNDLVYISHRAFSGLNSLEQLTLEKCNLTSIPTEALSHLHGLIVLRLRHLNINAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYGLNLTSLSITHCNLTAVPYLAVRHLVYLRFLNLSYNPISTIEGSMLHELLRLQEIQLVGGQLAVVEPYAFRGLNYLRVLNVSGNQLTTLEESVFHSVGNLETLILDSNPLACDCRLLWVFRRRWRLNFNRQQPTCATPEFVQGKEFKDFPDVLLPNYFTCRRARIRDRKAQQVFVDEGHTVQFVCRADGDPPPAILWLSPRKHLVSAKSNGRLTVFPDGTLEVRYAQVQDNGTYLCIAANAGGNDSMPAHLHVRS 477
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472     


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..ee.....eeeeeeeee........eeeeee.....eeeeeee......eee.......eeeeee....eeeeeee..hhhhheeeeeeee......eee...eeee.........eeeee..........eeeeeeeeeee.......ee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqt H   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSAYEMKWVRQAPGKGLEWVSVIGPSGGFTFYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCATEGDNDAFDIWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee............eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqt L   1 DIQMTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPMYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 214
                                    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)
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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 4OQT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LIGO1_HUMAN | Q96FE5: 2id5
        Q6PIL8_HUMAN | Q6PIL8: 5ug0
        S6B291_HUMAN | S6B291: 3mnw 3mnz 4eow 5c7k 5cus 5d9q 5veb 5vic 5vig 5viy 5vj6 5vob 5voc 5vod
UniProtKB/TrEMBL
        Q6PIL8_HUMAN | Q6PIL8: 1u6a 3dvg 3dvn 3eyq 3hi1
        S6B291_HUMAN | S6B291: 4llw 4lly 4ydv

(-) Related Entries Specified in the PDB File

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