3KDM - JenaLib

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Asym. Unit - sites (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN ANTI-STEROID FAB 5F2 IN COMPLEX WITH TESTOSTERONE

Authors :   M. H. Niemi, J. Rouvinen

Date :   23 Oct 09 (Deposition) - 26 May 10 (Release) - 07 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Immune System, Antibody, Immunoglobulin Fab Fragment, Anti-Steroid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. H. Niemi, K. Takkinen, L. K. Amundsen, H. Soderlund, J. Rouvinen, M. Hoyhtya
The Testosterone Binding Mechanism Of An Antibody Derived From A Naive Human Scfv Library
J. Mol. Recognit. V. 24 209 2010
PubMed-ID: 21360611 | Reference-DOI: 10.1002/JMR.1039

Molecule 1 - IMMUNOGLOBULIN LIGHT CHAIN
	Chains	:	L, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	RV308
	Expression System Taxid	:	562
	Expression System Vector	:	PKKTAC
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - IMMUNOGLOBULIN HEAVY CHAIN
	Chains	:	H, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	RV308
	Expression System Taxid	:	562
	Expression System Vector	:	PKKTAC
	Expression System Vector Type	:	PLASMID
	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 (2, 4)

No.	Name	Count	Type	Full Name
1	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID
2	TES	2	Ligand/Ion	TESTOSTERONE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
2	TES	1	Ligand/Ion	TESTOSTERONE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
2	TES	1	Ligand/Ion	TESTOSTERONE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP H:47 , TYR H:59 , ASP H:99 , TYR H:105 , GLY H:108 , PRO L:99 , TYR L:100	BINDING SITE FOR RESIDUE TES H 226
2	AC2	SOFTWARE	TRP B:47 , TYR B:59 , ASP B:99 , TYR B:105 , MET B:109	BINDING SITE FOR RESIDUE TES B 226

Asymmetric Unit

No.	Residues
1	A:22	-	A:90
2	A:138	-	A:198
3	B:22	-	B:96
4	B:149	-	B:205
5	H:22	-	H:96
6	H:149	-	H:205
7	L:22	-	L:90
8	L:138	-	L:198

Asymmetric Unit

No.	Residues
1	Tyr L:144	-	Pro L:145
2	Phe H:155	-	Pro H:156
3	Glu H:157	-	Pro H:158
4	Tyr A:144	-	Pro A:145
5	Phe B:155	-	Pro B:156
6	Glu B:157	-	Pro B:158

(no "SAP(SNP)/Variant" information available for 3KDM)

(no "PROSITE Motif" information available for 3KDM)

(no "Exon" information available for 3KDM)

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:216
                                                                                                                                                                                                                                                        
               SCOP domains d3kdma1 A:3-111 automated matches                                                                            d3kdma2 A:112-218 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------3kdmA02 A:113-218 Immunoglobulins                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee......eee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kdm A   3 ALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYGVTNRPSGVSNRFSGSKSGNTASLTISGLQAGDEADYYCSSYTSTRTPYVFGTGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3kdmB01 B:2-122 Immunoglobulins                                                                                          3kdmB02 B:123-222 Immunoglobulins                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee......eeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeee......eeeeee...hhhhheeeeeeee...........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdm B   1 xVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDPGLWDYYYGMDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSSVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPK 223
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
                            1-PCA

Chain H from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3kdmH01 H:2-122 Immunoglobulins                                                                                          3kdmH02 H:123-222 Immunoglobulins                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eeehhhhhh.eeeeee....eeeeee...hhhhheeeeeee............ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdm H   1 xVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDPGLWDYYYGMDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSSVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPK 223
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
                            1-PCA

Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d3kdml1 L:3-111 automated matches                                                                            d3kdml2 L:112-218 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------3kdmL02 L:113-218 Immunoglobulins                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeee......eee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kdm L   3 ALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYGVTNRPSGVSNRFSGSKSGNTASLTISGLQAGDEADYYCSSYTSTRTPYVFGTGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Human (Homo sapiens) [TaxId: 9606] (448)

1a	d3kdma1	A:3-111
1b	d3kdma2	A:112-218
1c	d3kdml1	L:3-111
1d	d3kdml2	L:112-218

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Homo sapiens. Organism_taxid: 9606. (14)

1a	3kdmA02	A:113-218
1b	3kdmB02	B:123-222
1c	3kdmH02	H:123-222
1d	3kdmL02	L:113-218
1e	3kdmB01	B:2-122
1f	3kdmH01	H:2-122

(no "Pfam Domain" information available for 3KDM)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3KDM)

Asymmetric Unit
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	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu B:157 - Pro B:158	[ RasMol ]
		Glu H:157 - Pro H:158	[ RasMol ]
		Phe B:155 - Pro B:156	[ RasMol ]
		Phe H:155 - Pro H:156	[ RasMol ]
		Tyr A:144 - Pro A:145	[ RasMol ]
		Tyr L:144 - Pro L:145	[ RasMol ]

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

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	3kdm
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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