1IJK: Von Willebrand factor

The von Willebrand Factor mutant (I546V) A1 domain-botrocetin Complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 10 Jul 2002.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Bothrops jararaca
Chains: 3
Atoms: 3,760
Mol. weight: 53.41 kDa
Released: 10 Jul 2002

Explore 1IJK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1IJK contains 16 α-helices and 30 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: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	509	1	1
β-strand	513-520	8	2
β-strand	522	1	3
α-helix	529-542	14
β-strand	544	1	1
β-strand	546	1	2
β-strand	551-558	8	2
β-strand	562-566	5	2
α-helix	574-582	9
β-strand	589	1	3
α-helix	594-600	7
α-helix	601-605	5
β-strand	615-622	8	2
α-helix	628-630	3
α-helix	634-643	10
β-strand	646-653	8	2
α-helix	659-668	10
β-strand	675-677	3	2
α-helix	687-695	9

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	4
β-strand	12-21	10	4
α-helix	23-32	10
β-strand	38-39	2	4
α-helix	48-57	10
β-strand	66-73	8	4
β-strand	83	1	5
α-helix	88	1
β-strand	89	1	5
α-helix	90	1
β-strand	95	1	6
α-helix	97-99	3
β-strand	103-107	5	4
β-strand	115-118	4	4
β-strand	124-130	7	4

Chain C: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	207-209	3	7
β-strand	212-221	10	7
α-helix	223-231	9
β-strand	238-239	2	7
α-helix	245-253	9
β-strand	264-265	2	7
β-strand	277-279	3	4
α-helix	287-289	3
β-strand	297-301	5	7
β-strand	308	1	6
β-strand	309-312	4	7
β-strand	317-324	8	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
von Willebrand factor	A	protein	202	Homo sapiens	P04275 (AlphaFold model)
Botrocetin	B	protein	133	Bothrops jararaca	P22029 (AlphaFold model)
Botrocetin	C	protein	125	Bothrops jararaca	P22030 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1IJK_1 von Willebrand factor (chains A)
SEPPLHDFYCSRLLDLVFLLDGSSRLSEAEFEVLKAFVVDMMERLRVSQKWVRVAVVEYH
DGSHAYIGLKDRKRPSELRRIASQVKYAGSQVASTSEVLKYTLFQIFSKIDRPEASRIAL
LLMASQEPQRMSRNFVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIEKQAPENKAFVLSS
VDELEQQRDEIVSYLCDLAPEA

Sequence of entity 2 (B), FASTA

>1IJK_2 Botrocetin (chains B)
DCPSGWSSYEGNCYKFFQQKMNWADAERFCSEQAKGGHLVSIKIYSKEKDFVGDLVTKNI
QSSDLYAWIGLRVENKEKQCSSEWSDGSSVSYENVVERTVKKCFALEKDLGFVLWINLYC
AQKNPFVCKSPPP

Sequence of entity 3 (C), FASTA

>1IJK_3 Botrocetin (chains C)
DCPPDWSSYEGHCYRFFKEWMHWDDAEEFCTEQQTGAHLVSFQSKEEADFVRSLTSEMLK
GDVVWIGLSDVWNKCRFEWTDGMEFDYDDYYLIAEYECVASKPTNNKWWIIPCTRFKNFV
CEFQA

Primary citation

Structural basis of von Willebrand factor activation by the snake toxin botrocetin. Fukuda, K., Doggett, T.A., Bankston, L.A. et al. Structure (2002) 10:943-950. DOI 10.1016/S0969-2126(02)00787-6 · 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
2ADF 1.9 Å, Crystal Structure and Paratope Determination of 82D6A3, an Antithrombotic Antibody…
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…

Browse structure collections

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