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(-) Description

Title :  CONTEXT-INDEPENDENT ANTI-HYPUSINE ANTIBODY FABHPU98 IN COMPLEX WITH DEOXYHYPUSINE
 
Authors :  Q. Zhai, P. J. Carter
Date :  18 Sep 15  (Deposition) - 20 Jan 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,H,L,P
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  H,L,P  (1x)
Keywords :  Deoxyhypusine, Antibody, Fabhpu98, Eif5A, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Zhai, M. He, A. Song, K. Deshayes, V. M. Dixit, P. J. Carter
Structural Analysis And Optimization Of Context-Independent Anti-Hypusine Antibodies.
J. Mol. Biol. V. 428 603 2016
PubMed-ID: 26778617  |  Reference-DOI: 10.1016/J.JMB.2016.01.006

(-) Compounds

Molecule 1 - FAB HPU98 HEAVY CHAIN
    Chains: A, H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 2 - FAB HPU98 LIGHT CHAIN
    Chains: B, L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 3
    Chains: P
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABHLP
Biological Unit 1 (1x): AB   
Biological Unit 2 (1x):   HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 30)

Asymmetric Unit (4, 30)
No.NameCountTypeFull Name
15GG1Mod. Amino AcidDEOXYHYPUSINE
2EDO14Ligand/Ion1,2-ETHANEDIOL
3PCA2Mod. Amino AcidPYROGLUTAMIC ACID
4SO413Ligand/IonSULFATE ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
15GG-1Mod. Amino AcidDEOXYHYPUSINE
2EDO10Ligand/Ion1,2-ETHANEDIOL
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID
4SO47Ligand/IonSULFATE ION
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
15GG1Mod. Amino AcidDEOXYHYPUSINE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID
4SO46Ligand/IonSULFATE ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:164 , THR A:165 , THR B:163 , ASN B:173binding site for residue EDO A 301
02AC2SOFTWARETHR A:87 , THR A:110 , PRO A:147 , GLU A:148 , TYR A:176binding site for residue EDO A 302
03AC3SOFTWAREPRO A:123 , ASN A:201 , LYS A:206 , THR A:207 , VAL A:208 , ALA A:209binding site for residue EDO A 303
04AC4SOFTWARELYS A:143 , GLN A:171 , SER A:172 , SER A:173binding site for residue EDO A 304
05AC5SOFTWARELYS A:203 , ASP A:205 , HOH A:468binding site for residue SO4 A 305
06AC6SOFTWAREARG A:164binding site for residue SO4 A 306
07AC7SOFTWAREARG A:10 , VAL A:12 , THR A:13 , THR A:16binding site for residue SO4 A 307
08AC8SOFTWARETHR A:72 , SER A:73 , LYS L:3binding site for residue SO4 A 308
09AC9SOFTWAREGLY A:118 , THR A:200 , THR A:202 , LYS A:206 , ASP B:123binding site for residue SO4 A 309
10AD1SOFTWARETHR B:114 , VAL B:115 , LEU B:116binding site for residue EDO B 301
11AD2SOFTWAREVAL B:143 , ASN B:160 , HOH B:420binding site for residue EDO B 302
12AD3SOFTWAREASN B:95C , ASN B:96 , HOH B:401binding site for residue EDO B 303
13AD4SOFTWARESER B:9 , TYR B:87 , GLY B:100 , GLY B:101binding site for residue EDO B 304
14AD5SOFTWARESER A:112 , ARG A:170 , GLN B:184 , SER B:187 , HOH B:408 , HOH B:468binding site for residue EDO B 305
15AD6SOFTWARELYS B:30 , ARG B:31 , SER B:67 , GLY B:68binding site for residue EDO B 306
16AD7SOFTWAREASN A:61 , ALA B:1 , ASN B:95C , SER H:172binding site for residue SO4 B 307
17AD8SOFTWARELYS B:39 , GLN B:42 , HOH B:417binding site for residue SO4 B 308
18AD9SOFTWAREPHE H:166 , PRO H:167 , SER H:177 , LEU H:178 , SER H:179 , SER L:175 , THR L:177binding site for residue EDO H 301
19AE1SOFTWARETHR H:87 , THR H:110 , PRO H:147 , GLU H:148 , TYR H:176binding site for residue EDO H 302
20AE2SOFTWAREGLY A:55 , ASN A:56 , HOH A:466 , LYS H:43 , GLY H:44 , GLU H:46 , HOH L:416binding site for residue EDO H 303
21AE3SOFTWAREPRO H:17 , LEU H:18 , THR H:19binding site for residue EDO H 304
22AE4SOFTWARETYR A:58 , LYS A:64 , HOH A:456 , SER B:95 , ASN B:95A , LYS H:43 , ARG H:170binding site for residue SO4 H 305
23AE5SOFTWAREGLN H:171 , SER H:172 , SER H:173binding site for residue SO4 H 306
24AE6SOFTWARELYS H:203 , ASP H:205binding site for residue SO4 H 307
25AE7SOFTWARELYS H:64 , SER L:95 , ASN L:95A , HOH L:418binding site for residue SO4 L 301
26AE8SOFTWARESER H:25 , GLY H:26 , SER H:100A , TYR L:49 , LYS L:53binding site for residue SO4 L 302
27AE9SOFTWARETYR H:52 , HOH L:422 , 5GG P:4binding site for residue SO4 P 101
28AF1SOFTWAREASN H:35 , ASP H:50 , TYR H:52 , ASP H:95 , TRP H:97 , TYR L:32 , GLY L:91 , TYR L:92 , SER L:94 , GLY P:5 , ALA P:6 , SO4 P:101binding site for Di-peptide GLY P 3 and 5GG P 4
29AF2SOFTWAREASN H:35 , ASP H:50 , TYR H:52 , ASP H:95 , TRP H:97 , ALA H:99 , TYR L:32 , GLY L:91 , TYR L:92 , SER L:94 , GLY P:3 , ALA P:6 , SO4 P:101binding site for Di-peptide 5GG P 4 and GLY P 5

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:127 -B:211
3A:140 -A:193
4B:23 -B:88
5B:80 -B:170
6B:134 -B:193
7H:22 -H:92
8H:140 -H:193
9L:23 -L:88
10L:80 -L:170
11L:134 -L:193

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:146 -Pro A:147
2Glu A:148 -Pro A:149
3Thr B:7 -Pro B:8
4Phe B:140 -Pro B:141
5Leu H:146 -Pro H:147
6Glu H:148 -Pro H:149
7Thr L:7 -Pro L:8
8Phe L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DUB)

(-) 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:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......eeeeeee......eeeeee.....eee.hhhh..eeeee...eeeeee...hhhhheeeeeeeeee....eeeeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee...eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dub A    2 xSVEESGGRLVTPGTPLTLTCTVSGFSLSTYTMNWVRQAPGKGLEWIGDIYTDGNTYYANWAKGRFTISKTSTTVDLKITSPTTEDTATYFCARDSWDASSYYGLDLWGQGTLVTVSSGQPKGPSVFPLAPCCSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSPVTCNVAHPATNTKVDKTVAP  210
                            |       11        21        31        41        51        61        71        81 |      90       100|||||  105       115       125  ||   139       149       159       169       179       191       201         
                            |                                                                              82A               100A||||                         128|                                                   187|                    
                            2-PCA                                                                                             100B|||                          133                                                    190                    
                                                                                                                               100C||                                                                                                        
                                                                                                                                100D|                                                                                                        
                                                                                                                                 100E                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..............eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dub B    1 AIKMTQTPSSVSAAVGGTVTINCQASEDIKRYLAWYQQKPGQPPKLLIYAASKLASGVSSRFKGSGSGTEYTLTISGVQCDDAATYYCQQGYTSSNVNNAFGGGTEVVVKGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC  211
                                    10        20        30        40        50        60        70        80        90     |||97       107       117       127       137       147       157       167       177       187       197       207    
                                                                                                                         95A||                                                                                                                    
                                                                                                                          95B|                                                                                                                    
                                                                                                                           95C                                                                                                                    


Chain H from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeee.....eee.hhhh..eeeee...eeeeee...hhhhheeeeeeee...........ee...eeeee........eeeee.......eeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeee....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dub H    2 xSVEESGGRLVTPGTPLTLTCTVSGFSLSTYTMNWVRQAPGKGLEWIGDIYTDGNTYYANWAKGRFTISKTSTTVDLKITSPTTEDTATYFCARDSWDASSYYGLDLWGQGTLVTVSSGQPKGPSVFPLAPCSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVSQPVTCNVAHPATNTKVDKTVAP  210
                            |       11        21        31        41        51        61        71        81 |      90       100|||||  105       115       125 ||    140       150       160       170       180   ||  193       203       
                            2-PCA                                                                          82A               100A||||                        127|                                                184|                      
                                                                                                                              100B|||                         133                                                 188                      
                                                                                                                               100C||                                                                                                      
                                                                                                                                100D|                                                                                                      
                                                                                                                                 100E                                                                                                      


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..............eeeeee......eeeee.....hhhh.eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dub L    1 AIKMTQTPSSVSAAVGGTVTINCQASEDIKRYLAWYQQKPGQPPKLLIYAASKLASGVSSRFKGSGSGTEYTLTISGVQCDDAATYYCQQGYTSSNVNNAFGGGTEVVVKGDPVAPTVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNR  208
                                    10        20        30        40        50        60        70        80        90     |||97       107       117       127       137       147       157       167       177       187       197       207 
                                                                                                                         95A||                                                                                                                 
                                                                                                                          95B|                                                                                                                 
                                                                                                                           95C                                                                                                                 


Chain P from PDB  Type:PROTEIN  Length:4
                                     
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                5dub P    3 GxGA    6
                             |  
                             4-5GG
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

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5drn 5ds8 5dsc 5dtf