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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CD45 EXTRACELLULAR REGION, DOMAINS D1-D4
 
Authors :  V. T. Chang, R. A. Fernandes, K. A. Ganzinger, S. F. Lee, C. Siebold, J. Mc P. Jonsson, M. Palayret, K. Harlos, C. H. Coles, E. Y. Jones, Y. Lui, E. H R. J. C. Gilbert, D. Klenerman, A. R. Aricescu, S. J. Davis
Date :  09 Nov 15  (Deposition) - 23 Mar 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Receptor Protein Tyrosine Phosphatase, Cd45, Ptprc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. T. Chang, R. A. Fernandes, K. A. Ganzinger, S. F. Lee, C. Siebold, J. Mccoll, P. Jonsson, M. Palayret, K. Harlos, C. H. Coles, E. Y. Jones, Y. Lui, E. Huang, R. J. Gilbert, D. Klenerman, A. R. Aricescu, S. J. Davis
Initiation Of T Cell Signaling By Cd45 Segregation At 'Close Contacts'.
Nat. Immunol. V. 17 574 2016
PubMed-ID: 26998761  |  Reference-DOI: 10.1038/NI.3392

(-) Compounds

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
    Cell: T-CELLS
    Chains: A, B
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO-K1
    Expression System Common: CHINESE HAMSTER
    Expression System Plasmid: PEE14
    Expression System Taxid: 10029
    Expression System Vector Type: PLASMID
    Fragment: DOMAINS D1-D4, RESIDUES 223-571
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LEUKOCYTE COMMON ANTIGEN, L-CA, T200, CD45 EXTRACELLULAR REGION D1-D4

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:527 , ARG A:528 , LEU A:542 , GLN A:543 , TYR A:548BINDING SITE FOR RESIDUE SO4 A1580
02AC2SOFTWAREARG A:515 , HIS A:532 , LYS A:533BINDING SITE FOR RESIDUE SO4 A1581
03AC3SOFTWAREARG B:515 , SER B:531 , HIS B:532 , LYS B:533BINDING SITE FOR RESIDUE SO4 B1579
04AC4SOFTWAREARG B:504 , ARG B:507BINDING SITE FOR RESIDUE SO4 B1580
05AC5SOFTWAREALA A:402 , ALA A:403 , HIS A:404 , GLN A:405BINDING SITE FOR RESIDUE SO4 A1582
06AC6SOFTWAREASN A:378 , ALA A:379BINDING SITE FOR MONO-SACCHARIDE NAG A1579 BOUND TO ASN A 378
07AC7SOFTWAREHIS A:418 , ASN A:419 , ASN A:434BINDING SITE FOR MONO-SACCHARIDE NAG A1575 BOUND TO ASN A 419
08AC8SOFTWARETHR A:421 , HIS A:458 , GLN A:466 , ASN A:468BINDING SITE FOR MONO-SACCHARIDE NAG A1578 BOUND TO ASN A 468
09AC9SOFTWARETRP A:487 , ASN A:488BINDING SITE FOR MONO-SACCHARIDE NAG A1577 BOUND TO ASN A 488
10BC1SOFTWAREGLU A:519 , ASN A:529BINDING SITE FOR MONO-SACCHARIDE NAG A1576 BOUND TO ASN A 529
11BC2SOFTWAREASP B:296 , ASN B:335 , TYR B:371 , ASN B:372BINDING SITE FOR MONO-SACCHARIDE NAG B1573 BOUND TO ASN B 335
12BC3SOFTWAREASN B:378BINDING SITE FOR MONO-SACCHARIDE NAG B1578 BOUND TO ASN B 378
13BC4SOFTWAREHIS B:418 , ASN B:419 , ASN B:434BINDING SITE FOR MONO-SACCHARIDE NAG B1576 BOUND TO ASN B 419
14BC5SOFTWAREGLU A:429 , ASP A:431 , THR B:421 , HIS B:458 , ASN B:468BINDING SITE FOR MONO-SACCHARIDE NAG B1577 BOUND TO ASN B 468
15BC6SOFTWARETRP B:487 , ASN B:488BINDING SITE FOR MONO-SACCHARIDE NAG B1575 BOUND TO ASN B 488
16BC7SOFTWAREGLU B:519 , ASN B:529BINDING SITE FOR MONO-SACCHARIDE NAG B1574 BOUND TO ASN B 529

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:226 -A:286
2A:258 -A:263
3A:274 -A:331
4A:309 -A:320
5A:342 -A:365
6A:398 -A:474
7A:423 -A:432
8A:503 -A:535
9B:226 -B:286
10B:258 -B:263
11B:274 -B:331
12B:309 -B:320
13B:342 -B:365
14B:398 -B:474
15B:423 -B:432
16B:503 -B:535

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:288 -Pro A:289
2Gly A:391 -Glu A:392
3Ala B:288 -Pro B:289

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FMV)

(-) 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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....eeeeee....eeeeee......ee........eeeee....eeeeeee........eeeeee...hhh.eeeee..hhhhh...eeeeeee......hhh.eeeeeee..eeee..eeee.......eeeeeeeeee..eeeeeeeeeee.........eeeeee......eeeeee.............................eeee.......eeeeeeeeeee...eee...eeeeee.........eeeeeee.....eeeeee...........eeeeeee...eeeeeee...eeee.......eeeeeeee.........eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fmv A 224 PTCDEKYANITVDYLYNKETKLFTAKLNVNENVECGNNTCTNNEVHNLTECKNASVSISHNSCTAPDKTLILDVPPGVEKFQLHDCTQVEKADTTICLKWKNIETFTCDTQNITYRFQCGNMIFDNKEIKLENLEPEHEYKCDSEILYNNHKFTNASKIIKTDFGSPGEPQIIFCRSEAAHQGVITWNPPQRSFHNFTLCYIKETEKDCLNLDKNLIKYDLQNLKPYTKYVLSLHAYIIAKVQRNGSAAMCHFTTKSAPPSQVWNMTVSMTSDNSMHVKCRPPRDRNGPHERYHLEVEAGNTLVRNESHKNCDFRVKDLQYSTDYTFKAYFHNGDYPGEPFILHHSTSGTK 574
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573 


Chain B from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee....eeeeee......ee....hhh.eeeee....eeeeeee........eeeeee...hhh.eeeee..hhhhh...eeeeeee......hhh.eeeeeee..eeee..eeee.......eeeeeeeeee..eeeeeeeeeee.........eeeeee......eeeeee.............................eeee.......eeeeeeeeeee...eee...eeeeee.........eeeeeee.....eeeeee...........eeeeeee...eeeeeee...eeee.......eeeeeeee.........eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fmv B 226 CDEKYANITVDYLYNKETKLFTAKLNVNENVECGNNTCTNNEVHNLTECKNASVSISHNSCTAPDKTLILDVPPGVEKFQLHDCTQVEKADTTICLKWKNIETFTCDTQNITYRFQCGNMIFDNKEIKLENLEPEHEYKCDSEILYNNHKFTNASKIIKTDFGSPGEPQIIFCRSEAAHQGVITWNPPQRSFHNFTLCYIKETEKDCLNLDKNLIKYDLQNLKPYTKYVLSLHAYIIAKVQRNGSAAMCHFTTKSAPPSQVWNMTVSMTSDNSMHVKCRPPRDRNGPHERYHLEVEAGNTLVRNESHKNCDFRVKDLQYSTDYTFKAYFHNGDYPGEPFILHHSTSG 572
                                   235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (43, 43)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        PTPRC_HUMAN | P08575: 1ygr 1ygu 5fn6 5fn7

(-) Related Entries Specified in the PDB File

5fn6 CRYSTAL STRUCTURE OF HUMAN CD45 EXTRACELLULAR REGION, DOMAINS D1-D3
5fn7 CRYSTAL STRUCTURE OF HUMAN CD45 EXTRACELLULAR REGION, DOMAINS D1-D2
5fn8 CRYSTAL STRUCTURE OF RAT CD45 EXTRACELLULAR REGION, DOMAINS D3-D4