2ADF: Von Willebrand factor

Crystal Structure and Paratope Determination of 82D6A3, an Antithrombotic Antibody Directed Against the von Willebrand factor A3-Domain. Determined by X-ray diffraction at 1.9 Å resolution. Released 6 Dec 2005.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 5,165
Mol. weight: 67.88 kDa
Released: 6 Dec 2005

Explore 2ADF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ADF contains 23 α-helices and 51 β-strands across 3 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 A: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	927-934	8	1
α-helix	941-957	17
β-strand	960	1	1
β-strand	965-972	8	1
β-strand	976-980	5	1
α-helix	988-996	9
α-helix	1007-1019	13
α-helix	1021-1023	3
β-strand	1030-1037	8	1
α-helix	1046-1054	9
β-strand	1057-1064	8	1
α-helix	1070-1076	7
α-helix	1078-1084	7
β-strand	1086-1088	3	1
α-helix	1093-1099	7
α-helix	1103-1109	7

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	2
β-strand	10-12	3	3
β-strand	18-25	8	2
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	46-51	6	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	2
α-helix	74-76	3
β-strand	78-83	6	2
α-helix	88-90	3
β-strand	92-100	9	3
β-strand	104-108	5	3
β-strand	112-116	5	3
α-helix	119-121	3
β-strand	122	1	4
α-helix	123-124	2
β-strand	125-129	5	5
β-strand	137	1	6
β-strand	140	1	6
β-strand	141-150	10	5
β-strand	151	1	4
β-strand	156-159	4	7
α-helix	160-162	3
β-strand	164	1	7
β-strand	168-176	9	5
β-strand	179-188	10	5
β-strand	199-204	6	7
α-helix	205-207	3
β-strand	209-214	6	7

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-13	4	9
β-strand	19-25	7	8
β-strand	33-38	6	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-90	7	9
β-strand	96-97	2	9
β-strand	101-105	5	9
β-strand	110	1	10
β-strand	113-117	5	11
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	11
β-strand	139	1	10
β-strand	144-149	6	12
β-strand	152-154	3	12
β-strand	158-162	5	11
α-helix	163-166	4
β-strand	172-181	10	11
α-helix	182-185	4
β-strand	191-196	6	12
β-strand	204-208	5	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Von Willebrand factor	A	protein	196	Homo sapiens	P04275 (AlphaFold model)
82D6A3 IgG	H	protein	218	Mus musculus	P01865 (AlphaFold model)
82D6A3 IgG	L	protein	209	Mus musculus	P01837 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2ADF_1 Von Willebrand factor (chains A)
GSHMAPDCSQPLDVILLLDGSSSFPASYFDEMKSFAKAFISKANIGPRLTQVSVLQYGSI
TTIDVPWNVVPEKAHLLSLVDVMQREGGPSQIGDALGFAVRYLTSEMHGARPGASKAVVI
LVTDVSVDSVDAAADAARSNRVTVFPIGIGDRYDAAQLRILAGPAGDSNVVKLQRIEDLP
TMVTLGNSFLHKLCSG

Sequence of entity 2 (H), FASTA

>2ADF_2 82D6A3 IgG (chains H)
QIQLVQSGPELKKPGETVKISCKASGYTFINYGMNWVKQAPGKGLKWMGWKNTNTGETTY
GEEFRGRFAFSLETSVSTAYLQINNLKNEDTATYFCARDNPYYALDYWGQGTTVTVSSAK
TTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Sequence of entity 3 (L), FASTA

>2ADF_3 82D6A3 IgG (chains L)
DIQMTQSPSSLSASLGGKVTITCKASQDINKYIAWYQHKPGKGPRLLIHYTSTLQPGIPS
RFSGSGSGRDYSFSISNLEPEDIATYYCLQYDNLRTFGGGTKLEIKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFN

Primary citation

Paratope determination of the antithrombotic antibody 82D6A3 based on the crystal structure of its complex with the von Willebrand factor A3-domain. Staelens, S., Hadders, M.A., Vauterin, S. et al. J Biol Chem (2006) 281:2225-2231. DOI 10.1074/jbc.M508191200 · PubMed

Other PDB entries of the same protein (UniProt P04275 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5BV8 1.59 Å, G1324S mutation in von Willebrand Factor A1 domain
7EOW 1.6 Å, High-resolution structure of vWF A1 domain in complex with caplacizumab, the first…
3ZQK 1.7 Å, Von Willebrand Factor A2 domain with calcium
1ATZ 1.8 Å, Human von willebrand factor A3 domain
1IJB 1.8 Å, The von Willebrand Factor mutant (I546V) A1 domain
3GXB 1.9 Å, Crystal structure of VWF A2 domain
3PPV 1.9 Å, Crystal structure of an engineered VWF A2 domain (N1493C and C1670S)
3PPW 1.9 Å, Crystal structure of the D1596A mutant of an engineered VWF A2 domain (N1493C and C1670S)
3PPX 1.91 Å, Crystal structure of the N1602A mutant of an engineered VWF A2 domain (N1493C and C1670S)
1FNS 2.0 Å, Crystal structure of the von willebrand factor (VWF) A1 domain I546V mutant in complex…
3PPY 2.0 Å, Crystal structure of the D1596A/N1602A double mutant of an engineered VWF A2 domain…
1FE8 2.03 Å, Crystal structure of the von willebrand factor A3 domain in complex with a FAB fragment…

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