Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  DEVELOPMENT AND PRECLINICAL CHARACTERIZATION OF A HUMANIZED ANTIBODY TARGETING CXCL12
 
Authors :  Z. Zhong, J. Wang, B. Li, H. Xiang, M. Ultsch, M. Coons, T Wong, N. Y. Chia S. Clark, R. Clark, L. Quintana, P. Gribling, E. Suto, K. Barck, R. Corp R. Takkar, W. P. Lee, L. A. Damico-Beyer, R. D. Carano, C. Adams, R. F. Ke W. Wang, N. Ferrara
Date :  10 Jul 13  (Deposition) - 14 Aug 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.77
Chains :  Asym. Unit :  D,E,F,H,I,L
Biol. Unit 1:  D,H,L  (1x)
Biol. Unit 2:  E,F,I  (1x)
Keywords :  Immunoglobulin, Cell Adhesion-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zhong, J. Wang, B. Li, H. Xiang, M. Ultsch, M. Coons, T. Wong, N. Y. Chiang, S. Clark, R. Clark, L. Quintana, P. Gribling, E. Suto, K. Barck, R. Corpuz, J. Yao, R. Takkar, W. P. Lee, L. A. Damico-Beyer, R. D. Carano, C. Adams, R. F. Kelley, W. Wang, N. Ferrara
Development And Preclinical Characterization Of A Humanized Antibody Targeting Cxcl12.
Clin. Cancer Res. V. 19 4433 2013
PubMed-ID: 23812669  |  Reference-DOI: 10.1158/1078-0432.CCR-13-0943

(-) Compounds

Molecule 1 - STROMAL CELL-DERIVED FACTOR 1
    Chains: D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CXCL12, SDF1, SDF1A, SDF1B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SDF-1, HSDF-1, C-X-C MOTIF CHEMOKINE 12, INTERCRINE REDUCED IN HEPATOMAS, IRH, HIRH, PRE-B CELL GROWTH-STIMULATING FACTOR, PBSF, SDF-1-BETA(3-72), SDF-1-ALPHA(3-67)
 
Molecule 2 - IMMUNOGLOBULIN G1 HEAVY CHAIN
    Chains: E, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 29-89
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - STROMAL CELL-DERIVED FACTOR 1
    Chains: I, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CXCL12, SDF1, SDF1A, SDF1B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SDF-1, HSDF-1, C-X-C MOTIF CHEMOKINE 12, INTERCRINE REDUCED IN HEPATOMAS, IRH, HIRH, PRE-B CELL GROWTH-STIMULATING FACTOR, PBSF, SDF-1-BETA(3-72), SDF-1-ALPHA(3-67)

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : DEFHIL
Biological Unit 1 (1x): D  H L
Biological Unit 2 (1x):  EF I 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4LMQ)

(-) Sites  (0, 0)

(no "Site" information available for 4LMQ)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1D:11 -D:50
2E:22 -E:92
3F:9 -F:34
4F:11 -F:50
5H:22 -H:92
6H:140 -H:196
7I:23 -I:88
8I:134 -I:194
9L:23 -L:88
10L:134 -L:194

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Ser E:54 -Gly E:55
2Glu F:15 -Ser F:16
3Ser F:16 -His F:17
4Ser H:54 -Gly H:55
5Ser H:128 -Lys H:129
6Phe H:146 -Pro H:147
7Glu H:148 -Pro H:149
8Ser H:188 -Leu H:189
9Ser I:7 -Pro I:8
10Thr I:94 -Pro I:95
11Tyr I:140 -Pro I:141
12Ser L:7 -Pro L:8
13Thr L:94 -Pro L:95
14Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LMQ)

(-) 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 D from PDB  Type:PROTEIN  Length:55
                                                                                        
               SCOP domains d4lmqd_ D: automated matches                            SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhh.eeeeeee.....eeeee.....eee....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                4lmq D   11 CRFFESHVARANVKHLKILNTPLQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK   68
                                    20        30 ||     43        53        63     
                                                32|                                
                                                 36                                


Chain E from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee...eeeeeeee.....eee.......ee..ee....eeeeee...hhhhheeeeeeee........eeee...eeeee......eeeee.eeeeeeee.....eeee.........ee...ee.....eeeeeee.eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lmq E    1 EVQLVESGGGLVQPGGSLRLSCAASGFSLTVYSVHWVRQAPGKGLEWVGALWGSGGTEYNSNLKSRFTISRDTSKNTVYLQMNSLRAEDTAVYYCARDQGLNYGSLFDYWGQGTLVTVSSASGPSVFPLALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||103       113 ||    137       147       157       167       177    || 198       208     
                                                                                                            82A||               100A|||            115|   124|                                          182|                   
                                                                                                             82B|                100B||             118    137                                           194                   
                                                                                                              82C                 100C|                                                                                        
                                                                                                                                   100D                                                                                        


Chain F from PDB  Type:PROTEIN  Length:58
                                                                                           
               SCOP domains d4lmqf_ F: automated matches                               SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee...hhh.eeeeee.........eeeee.....eeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                4lmq F    8 RCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKA   65
                                    17        27        37        47        57        


Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee........eeeeee.....eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee..........eeeeeeeeee........eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lmq H    1 EVQLVESGGGLVQPGGSLRLSCAASGFSLTVYSVHWVRQAPGKGLEWVGALWGSGGTEYNSNLKSRFTISRDTSKNTVYLQMNSLRAEDTAVYYCARDQGLNYGSLFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||103       113       123       133       143       153       163       173       183       193       203       213
                                                                                                            82A||               100A|||                                                                                                                 
                                                                                                             82B|                100B||                                                                                                                 
                                                                                                              82C                 100C|                                                                                                                 
                                                                                                                                   100D                                                                                                                 


Chain I from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d4lmqi1 I:1-107 automated matches                                                                          d4lmqi2 I:108-214 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.ee..ee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.......eeee..ee....ee............eeeeeeeeeehhhhh...eeeee...........eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lmq I    1 DIQMTQSPSSLSASVGDRVTITCRASESISYSLSWYQQKPGKAPKLLIYNAVKLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCKQYWNTPFTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d4lmql1 L:1-107 automated matches                                                                          d4lmql2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh....eeeeee.......eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lmq L    1 DIQMTQSPSSLSASVGDRVTITCRASESISYSLSWYQQKPGKAPKLLIYNAVKLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCKQYWNTPFTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  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)
  - → 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
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (50, 50)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4lmq)
 
  Sites
(no "Sites" information available for 4lmq)
 
  Cis Peptide Bonds
    Glu F:15 - Ser F:16   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser E:54 - Gly E:55   [ RasMol ]  
    Ser F:16 - His F:17   [ RasMol ]  
    Ser H:128 - Lys H:129   [ RasMol ]  
    Ser H:188 - Leu H:189   [ RasMol ]  
    Ser H:54 - Gly H:55   [ RasMol ]  
    Ser I:7 - Pro I:8   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Thr I:94 - Pro I:95   [ RasMol ]  
    Thr L:94 - Pro L:95   [ RasMol ]  
    Tyr I:140 - Pro I:141   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4lmq
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SDF1_HUMAN | P48061
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SDF1_HUMAN | P48061
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SDF1_HUMAN | P48061: 1a15 1qg7 1sdf 1vmc 2j7z 2k01 2k03 2k04 2k05 2kec 2ked 2kee 2kol 2n55 2nwg 2sdf 3gv3 3hp3 4uai

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4LMQ)