5C6W: Anti-CXCL13 scFv - E10

anti-CXCL13 scFv - E10. Determined by X-ray diffraction at 1.54 Å resolution. Released 4 Nov 2015.

Method: X-ray diffraction
Resolution: 1.54 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,436
Mol. weight: 57.69 kDa
Released: 4 Nov 2015

Explore 5C6W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C6W contains 10 α-helices and 57 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain H: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	33-39	7	2
β-strand	41	1	3
β-strand	45-52	8	2
β-strand	57-60	4	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	102-104	3	4
β-strand	107-109	3	4
β-strand	116-117	2	2
β-strand	121-125	5	2
α-helix	1002-1003	2
β-strand	1004	1	5
β-strand	1005	1	6
β-strand	1009-1012	4	7
β-strand	1018-1023	6	6
β-strand	1035-1040	6	7
β-strand	1047-1050	4	7
β-strand	1051	1	8
β-strand	1055	1	8
α-helix	1056-1057	2
β-strand	1064-1069	6	6
β-strand	1072-1077	6	6
α-helix	1082-1084	3
β-strand	1086-1093	8	7
β-strand	1099-1101	3	7
β-strand	1102	1	5
β-strand	1105-1109	5	7

Chain J: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
α-helix	7-9	3
β-strand	10-12	3	10
β-strand	18-25	8	9
β-strand	33-39	7	10
β-strand	41	1	3
β-strand	45-52	8	10
β-strand	57-60	4	10
β-strand	65	1	9
β-strand	68-73	6	9
α-helix	74-76	3
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	102-104	3	11
β-strand	107-109	3	11
β-strand	116-117	2	10
β-strand	121-125	5	10
α-helix	1002-1003	2
β-strand	1004	1	12
β-strand	1005	1	13
β-strand	1009-1012	4	14
β-strand	1018-1023	6	13
β-strand	1035-1040	6	14
β-strand	1047-1050	4	14
β-strand	1051	1	15
β-strand	1055	1	15
β-strand	1064-1069	6	13
β-strand	1072-1077	6	13
α-helix	1082-1084	3
β-strand	1086-1093	8	14
β-strand	1099-1101	3	14
β-strand	1102	1	12
β-strand	1105-1109	5	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein IGHV1-69-2,Ig lambda chain V-II region NIG-84	H, J	protein	264	Homo sapiens	A0A0B4J2H0 (AlphaFold model), P01704 (AlphaFold model)

Sequence of entity 1 (H, J), FASTA

>5C6W_1 Protein IGHV1-69-2,Ig lambda chain V-II region NIG-84 (chains H, J)
QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANY
AQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCAREPDYYDSSGYYPIDAFDIWGQG
TTVTVSSGGGGSGGGGSGGGGSQSALTQPASVSASPGQSITISCTGTSSDVGAYDWVSWY
QQHPGKAPKLLIFDVNNRPSGVSHRFSGSKSGNTASLTISGLQAEDEADYYCASATLLDT
YVFGTGTKVTVLGDQEPKSSDKTH

Primary citation

Optimization of a scFv-based biotherapeutic by CDR side-chain clash repair. Tu, C., Terraube, V., Tam, A. et al. To be published.

Other PDB entries of the same protein (UniProt A0A0B4J2H0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5C2B 1.4 Å, anti-CXCL13 parental scFv - 3B4
5WKZ 1.85 Å, VH1-69 germline antibody predicted from CR6261
5CBE 2.4 Å, E10 in complex with CXCL13
5CBA 2.5 Å, 3B4 in complex with CXCL13 - 3B4-CXCL13

Browse structure collections

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