5I1D - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV3-23/IGKV4-1

Authors :   A. Teplyakov, G. Obmolova, T. Malia, J. Luo, G. Gilliland

Date :   05 Feb 16 (Deposition) - 24 Feb 16 (Release) - 03 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Monoclonal Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Teplyakov, G. Obmolova, T. J. Malia, J. Luo, S. Muzammil, R. Sweet, J. C. Almagro, G. L. Gilliland
Structural Diversity In A Human Antibody Germline Library.
Mabs V. 8 1045 2016
PubMed-ID: 27210805 | Reference-DOI: 10.1080/19420862.2016.1190060
(for further references see the PDB file header)

Molecule 1 - FAB LIGHT CHAIN
	Chains	:	L, A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - FAB HEAVY CHAIN
	Chains	:	H, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN L:43 , LYS L:45 , GLN L:48 , HOH L:429	binding site for residue SO4 L 301
2	AC2	SOFTWARE	LYS A:45 , GLN A:48 , HOH A:430 , HOH A:466	binding site for residue SO4 A 301
3	AC3	SOFTWARE	ALA B:120 , SER B:121 , HOH B:1044 , HOH B:1058 , HOH B:1081 , GLN L:153 , LYS L:155 , HOH L:425 , HOH L:456 , HOH L:473	binding site for residue SO4 B 901

Asymmetric Unit

No.	Residues
1	A:23	-	A:94
2	A:140	-	A:200
3	B:22	-	B:96
4	B:146	-	B:202
5	H:22	-	H:96
6	H:146	-	H:202
7	L:23	-	L:94
8	L:140	-	L:200
9	L:220	-	H:222

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Thr L:100	-	Pro L:101
3	Tyr L:146	-	Pro L:147
4	Phe H:152	-	Pro H:153
5	Glu H:154	-	Pro H:155
6	Ser A:7	-	Pro A:8
7	Thr A:100	-	Pro A:101
8	Tyr A:146	-	Pro A:147
9	Phe B:152	-	Pro B:153
10	Glu B:154	-	Pro B:155

(no "SAP(SNP)/Variant" information available for 5I1D)

(no "PROSITE Motif" information available for 5I1D)

(no "Exon" information available for 5I1D)

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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i1d A   1 DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee...eeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i1d B   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKYDGELDFWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 219
                                    10        20        30        40        50        60        70        80        90       100|      113       123       133|      149       159       169       179       189       199       209       219
                                                                                                                             100|                          133|                                                                               
                                                                                                                              104                           140

Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i1d H   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKYDGIYGELDFWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   146       156       166       176       186       196       206       216      
                                                                                                                                                              133|                                                                                  
                                                                                                                                                               140

Chain L from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i1d L   1 DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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 5I1D, only for superseded entry 3QOS replaced by 5I1D)

(no "CATH Domain" information available for 5I1D)

(no "Pfam Domain" information available for 5I1D)

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(no "Gene Ontology" information available for 5I1D)

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	Cis Peptide Bonds
		Glu B:154 - Pro B:155	[ RasMol ]
		Glu H:154 - Pro H:155	[ RasMol ]
		Phe B:152 - Pro B:153	[ RasMol ]
		Phe H:152 - Pro H:153	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Thr A:100 - Pro A:101	[ RasMol ]
		Thr L:100 - Pro L:101	[ RasMol ]
		Tyr A:146 - Pro A:147	[ RasMol ]
		Tyr L:146 - Pro L:147	[ RasMol ]

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

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Description

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Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (9, 9)

Cis Peptide Bonds (10, 10)

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