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(-) Description

Title :  CRYSTAL STRUCTURE OF A CHEMOENZYMATIC GLYCOENGINEERED DISIALYLATED FC (DI-SFC)
 
Authors :  A. A. Ahmed, J. Giddens, A. Pincetic, J. V. Lomino, J. V. Ravetch, L. X. Wa P. J. Bjorkman
Date :  23 Apr 14  (Deposition) - 23 Jul 14  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Ahmed, J. Giddens, A. Pincetic, J. V. Lomino, J. V. Ravetch, L. X. Wang, P. J. Bjorkman
Structural Characterization Of Anti-Inflammatory Immunoglobulin G Fc Proteins.
J. Mol. Biol. V. 426 3166 2014
PubMed-ID: 25036289  |  Reference-DOI: 10.1016/J.JMB.2014.07.006

(-) Compounds

Molecule 1 - IG GAMMA-1 CHAIN C REGION
    Chains: A, B, C, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293-6E
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 109-329
    Gene: IGHG1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 33)

Asymmetric Unit (5, 33)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2GAL3Ligand/IonBETA-D-GALACTOSE
3MAN8Ligand/IonALPHA-D-MANNOSE
4NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA2Ligand/IonO-SIALIC ACID
Biological Unit 1 (5, 16)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA1Ligand/IonO-SIALIC ACID
Biological Unit 2 (5, 17)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:265 , GLN A:295 , ASN A:297 , NAG A:502 , MAN B:508BINDING SITE FOR RESIDUE NAG A 501
02AC2SOFTWAREPHE A:241 , VAL A:264 , NAG A:501 , BMA A:503 , MAN A:504 , MAN B:508BINDING SITE FOR RESIDUE NAG A 502
03AC3SOFTWAREPHE A:243 , NAG A:502 , MAN A:504 , MAN A:506BINDING SITE FOR RESIDUE BMA A 503
04AC4SOFTWARENAG A:502 , BMA A:503 , NAG A:505BINDING SITE FOR RESIDUE MAN A 504
05AC5SOFTWAREMAN A:504BINDING SITE FOR RESIDUE NAG A 505
06AC6SOFTWAREBMA A:503 , NAG A:507 , BMA B:503BINDING SITE FOR RESIDUE MAN A 506
07AC7SOFTWAREMAN A:506BINDING SITE FOR RESIDUE NAG A 507
08AC8SOFTWAREASP B:265 , GLN B:295 , ASN B:297 , THR B:299 , NAG B:502BINDING SITE FOR RESIDUE NAG B 501
09AC9SOFTWAREPHE B:241 , ARG B:301 , NAG B:501 , BMA B:503 , MAN B:504BINDING SITE FOR RESIDUE NAG B 502
10BC1SOFTWAREMAN A:506 , PHE B:241 , PHE B:243 , NAG B:502 , MAN B:504 , MAN B:508BINDING SITE FOR RESIDUE BMA B 503
11BC2SOFTWARENAG B:502 , BMA B:503 , NAG B:505BINDING SITE FOR RESIDUE MAN B 504
12BC3SOFTWARETHR B:260 , MAN B:504 , GAL B:506BINDING SITE FOR RESIDUE NAG B 505
13BC4SOFTWAREPRO B:244 , LYS B:246 , ASP B:249 , GLU B:258 , THR B:260 , NAG B:505 , SIA B:507BINDING SITE FOR RESIDUE GAL B 506
14BC5SOFTWAREGAL B:506BINDING SITE FOR RESIDUE SIA B 507
15BC6SOFTWARENAG A:501 , NAG A:502 , BMA B:503 , NAG B:509BINDING SITE FOR RESIDUE MAN B 508
16BC7SOFTWAREMAN B:508BINDING SITE FOR RESIDUE NAG B 509
17BC8SOFTWAREASN C:297 , THR C:299 , NAG C:502BINDING SITE FOR RESIDUE NAG C 501
18BC9SOFTWAREPHE C:241 , PHE C:243 , NAG C:502 , MAN C:504 , MAN C:507BINDING SITE FOR RESIDUE BMA C 503
19CC1SOFTWARENAG C:502 , BMA C:503 , NAG C:505BINDING SITE FOR RESIDUE MAN C 504
20CC2SOFTWAREPHE C:243 , THR C:260 , MAN C:504 , GAL C:506BINDING SITE FOR RESIDUE NAG C 505
21CC3SOFTWAREPHE C:243 , PRO C:244 , GLU C:258 , THR C:260 , NAG C:505 , SIA C:509BINDING SITE FOR RESIDUE GAL C 506
22CC4SOFTWAREPHE C:241 , NAG C:501 , BMA C:503 , MAN C:504BINDING SITE FOR RESIDUE NAG C 502
23CC5SOFTWAREBMA C:503 , NAG C:508BINDING SITE FOR RESIDUE MAN C 507
24CC6SOFTWAREMAN C:507BINDING SITE FOR RESIDUE NAG C 508
25CC7SOFTWAREGAL C:506BINDING SITE FOR RESIDUE SIA C 509
26CC8SOFTWAREASN D:297 , NAG D:502BINDING SITE FOR RESIDUE NAG D 501
27CC9SOFTWARENAG D:501 , BMA D:503 , MAN D:506BINDING SITE FOR RESIDUE NAG D 502
28DC1SOFTWAREPHE D:243 , NAG D:502 , MAN D:504 , MAN D:506BINDING SITE FOR RESIDUE BMA D 503
29DC2SOFTWAREPHE D:241 , BMA D:503 , NAG D:505BINDING SITE FOR RESIDUE MAN D 504
30DC3SOFTWAREPHE D:241 , MAN D:504BINDING SITE FOR RESIDUE NAG D 505
31DC4SOFTWARENAG D:502 , BMA D:503 , NAG D:507BINDING SITE FOR RESIDUE MAN D 506
32DC5SOFTWARELYS D:246 , THR D:260 , MAN D:506 , GAL D:508BINDING SITE FOR RESIDUE NAG D 507
33DC6SOFTWAREASP D:249 , GLU D:258 , THR D:260 , NAG D:507BINDING SITE FOR RESIDUE GAL D 508

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:261 -A:321
2A:367 -A:425
3B:261 -B:321
4B:367 -B:425
5C:261 -C:321
6C:367 -C:425
7D:261 -D:321
8D:367 -D:425

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Glu A:293 -Glu A:294
2Gln A:295 -Tyr A:296
3Pro A:329 -Ala A:330
4Tyr A:373 -Pro A:374
5Glu B:293 -Glu B:294
6Tyr B:373 -Pro B:374
7His C:268 -Glu C:269
8His C:285 -Asn C:286
9Tyr C:373 -Pro C:374
10Pro D:291 -Arg D:292
11Tyr D:373 -Pro D:374

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q6Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q6Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q6Y)

(-) 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:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhh.....eeeeeee.........eeeeee..eee...ee............eeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeee........eee...ee.....eeeeeeeeeehhhhh....eeeeee...hhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q6y A 236 GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL 443
                                   245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435        


Chain B from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhh.....eeeeeee.........eeeeee..eee...eee..........eeeeeee.hhhhhhh...eeeeee......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q6y B 238 PSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS 444
                                   247       257       267       277       287       297       307       317       327 ||    338       348       358       368       378       388       398       408       418       428       438      
                                                                                                                     329|                                                                                                                 
                                                                                                                      331                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhh.....eeeeee..........eeeeee..eee...ee.............eeeee.hhhhhhh...eeeeee..eee..........eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeeee..hhhhheeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q6y C 238 PSVFLFPPKPKDTLMSRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS 444
                                   247    || 258       268       278       288       298       308       318      |335       345       355       365       375       385       395       405       415       425       435         
                                        252|                                                                    325|                                                                                                               
                                         254                                                                     333                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..hhhhhhh.....eeeeee....eeeee..eee...eee........eeeeee.hhhhhhh...eeeee.......eeeee..........eeeee..hhhhh...eeeeeeeeeee.....eeeeee..eee..eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q6y D 238 PSVFLFPPKPKDTLMISRTPEVTCVVPEVKFNWYVDGVEVHNAKTKPREEQYNRVVSVLTVLHQDWLNGKEYKCKVSKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL 443
                                   247       257     ||274       284       294  ||   307       317      |328       338       348       358       368       378       388       398       408       418       428       438     
                                                   263|                       297|                    324|                                                                                                                     
                                                    271                        301                     326
   Legend:   → Mismatch (orange background)
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    → 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 4Q6Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q6Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q6Y)

(-) Gene Ontology  (20, 20)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IGHG1_HUMAN | P01857: 1aj7 1aqk 1axs 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 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

(-) Related Entries Specified in the PDB File

4q74 4q7d