5DS8 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CONTEXT-INDEPENDENT ANTI-HYPUSINE ANTIBODY FABHPU98 IN COMPLEX WITH HYPUSINE

Authors :   Q. Zhai, P. J. Carter

Date :   17 Sep 15 (Deposition) - 20 Jan 16 (Release) - 04 May 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A,B,H,L,P
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: H,L,P  (1x)

Keywords :   Hypusine, 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

Molecule 1 - FAB HPU98 HEAVY CHAIN
	Chains	:	A, H
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Taxid	:	10029
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986

Molecule 2 - FAB HOU98 LIGHT CHAIN
	Chains	:	B, L
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Taxid	:	10029
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986

Molecule 3 - TETRAPEPTIDE GLY-HPU-GLY-ALA
	Chains	:	P
	Engineered	:	YES
	Expression System	:	SYNTHEMIS
	Expression System Taxid	:	448016
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630

		1	2	3	4	5
Asymmetric Unit	:	A	B	H	L	P
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			H	L	P

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 19)

No.	Name	Count	Type	Full Name
1	5CT	1	Mod. Amino Acid	HYPUSINE
2	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
3	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID
4	SO4	11	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	5CT	-1	Mod. Amino Acid	HYPUSINE
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
4	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 9)

No.	Name	Count	Type	Full Name
1	5CT	1	Mod. Amino Acid	HYPUSINE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
4	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:200 , THR A:202 , LYS A:206 , ASP B:123	binding site for residue EDO A 301
02	AC2	SOFTWARE	ARG A:164 , THR A:165 , THR B:163 , ASN B:173	binding site for residue EDO A 302
03	AC3	SOFTWARE	THR A:87 , THR A:110 , PRO A:147 , GLU A:148 , TYR A:176	binding site for residue EDO A 303
04	AC4	SOFTWARE	ARG A:164	binding site for residue SO4 A 304
05	AC5	SOFTWARE	THR A:72 , SER A:73	binding site for residue SO4 A 305
06	AC6	SOFTWARE	LYS A:64 , SER B:95 , ASN B:95A , HOH B:471 , ARG H:170	binding site for residue SO4 B 301
07	AC7	SOFTWARE	SER A:112 , ARG A:170 , GLN B:184 , SER B:187 , HOH B:411	binding site for residue SO4 B 302
08	AC8	SOFTWARE	GLN B:37 , LYS B:39 , GLN B:42 , HOH B:401 , HOH B:403	binding site for residue SO4 B 303
09	AC9	SOFTWARE	GLU B:27 , TYR B:92 , HOH B:402 , SER H:112 , HOH H:406	binding site for residue SO4 B 304
10	AD1	SOFTWARE	PHE H:166 , PRO H:167 , LEU H:178 , SER H:179 , SER L:161 , SER L:175 , THR L:177	binding site for residue EDO H 301
11	AD2	SOFTWARE	THR H:87 , THR H:110 , PRO H:147 , GLU H:148 , TYR H:176	binding site for residue EDO H 302
12	AD3	SOFTWARE	GLN H:171 , SER H:172 , SER H:173	binding site for residue SO4 H 303
13	AD4	SOFTWARE	SER H:25 , SER H:100A , TYR L:49 , LYS L:53	binding site for residue SO4 H 304
14	AD5	SOFTWARE	LYS H:203 , ASP H:205	binding site for residue SO4 H 305
15	AD6	SOFTWARE	LYS H:64 , SER L:95 , ASN L:95A , HOH L:408	binding site for residue SO4 L 301
16	AD7	SOFTWARE	TYR H:52 , TYR L:92 , HOH L:414	binding site for residue SO4 P 101

Asymmetric Unit

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

Asymmetric Unit

No.	Residues
1	Leu A:146	-	Pro A:147
2	Glu A:148	-	Pro A:149
3	Thr B:7	-	Pro B:8
4	Phe B:140	-	Pro B:141
5	Leu H:146	-	Pro H:147
6	Glu H:148	-	Pro H:149
7	Ala H:209	-	Pro H:210
8	Thr L:7	-	Pro L:8
9	Phe L:140	-	Pro L:141

(no "SAP(SNP)/Variant" information available for 5DS8)

(no "PROSITE Motif" information available for 5DS8)

(no "Exon" information available for 5DS8)

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:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......eeeeeee......eeeeee.....eee.hhhh..eeeee...eeeeee...hhhhheeeeeeee...........ee...eeeee........eeeee.....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ds8 A    2 xSVEESGGRLVTPGTPLTLTCTVSGFSLSTYTMNWVRQAPGKGLEWIGDIYTDGNTYYANWAKGRFTISKTSTTVDLKITSPTTEDTATYFCARDSWDASSYYGLDLWGQGTLVTVSSGQPKGPSVFPLAPCSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSQPVTCNVAHPATNTKVDKTVAP  210
                            |       11        21        31        41        51        61        71        81 |      90       100|||||  105       115       125 ||    141       151       161       171       181    || 193       203       
                            |                                                                              82A               100A||||                        127|                                                 186|                     
                            2-PCA                                                                                             100B|||                         134                                                  189                     
                                                                                                                               100C||                                                                                                      
                                                                                                                                100D|                                                                                                      
                                                                                                                                 100E

Chain B 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..hhhhhh..eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ds8 B    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 H from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                             
               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....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5ds8 H    2 xSVEESGGRLVTPGTPLTLTCTVSGFSLSTYTMNWVRQAPGKGLEWIGDIYTDGNTYYANWAKGRFTISKTSTTVDLKITSPTTEDTATYFCARDSWDASSYYGLDLWGQGTLVTVSSGQPKGPSVFPLAPCTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTPVTCNVAHPATNTKVDKTVAP  210
                            |       11        21        31        41        51        61        71        81 |      90       100|||||  105       115       125 ||    142       152       162       172       182  ||   196       206    
                            2-PCA                                                                          82A               100A||||                        127|                                               185|                    
                                                                                                                              100B|||                         135                                                190                    
                                                                                                                               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.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ds8 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
                5ds8 P    3 GxGA    6
                             |  
                             4-5CT

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 '\|'

(no "SCOP Domain" information available for 5DS8)

(no "CATH Domain" information available for 5DS8)

(no "Pfam Domain" information available for 5DS8)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 5DS8)

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
		5CT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PCA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		AD1	[ RasMol ]	+environment [ RasMol ]
		AD2	[ RasMol ]	+environment [ RasMol ]
		AD3	[ RasMol ]	+environment [ RasMol ]
		AD4	[ RasMol ]	+environment [ RasMol ]
		AD5	[ RasMol ]	+environment [ RasMol ]
		AD6	[ RasMol ]	+environment [ RasMol ]
		AD7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala H:209 - Pro H:210	[ RasMol ]
		Glu A:148 - Pro A:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Leu A:146 - Pro A:147	[ RasMol ]
		Leu H:146 - Pro H:147	[ RasMol ]
		Phe B:140 - Pro B:141	[ RasMol ]
		Phe L:140 - Pro L:141	[ RasMol ]
		Thr B:7 - Pro B:8	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites 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)

Access by PDB/NDB ID
	5ds8
		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
	(no 'UniProt ID/Accession number' available) \|
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProt

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

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
	(no 'UniProt ID/Accession number' available) \|
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT

(no "Entries Sharing at Least One Protein Chain" available for 5DS8)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (16, 16)

SS Bonds (10, 10)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File