3ZQK: Von Willebrand Factor A2 domain with calcium

Von Willebrand Factor A2 domain with calcium. Determined by X-ray diffraction at 1.7 Å resolution. Released 27 Jul 2011.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 5,099
Mol. weight: 67.41 kDa
Ligands: NAG, CA
Released: 27 Jul 2011

Explore 3ZQK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3ZQK contains 26 α-helices and 22 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1498-1504	7	1
α-helix	1511-1527	17
β-strand	1530	1	2
β-strand	1535	1	2
β-strand	1536-1542	7	1
β-strand	1546-1550	5	1
α-helix	1558-1567	10
α-helix	1578-1584	7
α-helix	1585-1589	5
α-helix	1592-1594	3
β-strand	1602-1608	7	1
β-strand	1623-1630	8	1
α-helix	1636-1643	8
α-helix	1647-1648	2
β-strand	1649-1651	3	1
α-helix	1657-1670	14

Chain B: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1497-1504	8	3
α-helix	1510-1527	18
β-strand	1530	1	3
β-strand	1535-1542	8	3
β-strand	1546-1550	5	3
α-helix	1558-1565	8
α-helix	1578-1584	7
α-helix	1585-1589	5
α-helix	1592-1594	3
β-strand	1602-1608	7	3
α-helix	1618-1620	3
β-strand	1623-1630	8	3
α-helix	1636-1643	8
α-helix	1647-1648	2
β-strand	1649-1651	3	3
α-helix	1657-1668	12

Chain C: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1497-1504	8	4
α-helix	1510-1527	18
β-strand	1530	1	4
β-strand	1535-1542	8	4
β-strand	1546-1550	5	4
α-helix	1558-1566	9
α-helix	1568-1570	3
α-helix	1578-1584	7
α-helix	1585-1589	5
α-helix	1592-1594	3
β-strand	1602-1608	7	4
β-strand	1623-1630	8	4
α-helix	1636-1643	8
α-helix	1647-1648	2
β-strand	1649-1651	3	4
α-helix	1657-1669	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Von willebrand factor	A, B, C	protein	199	HOMO SAPIENS	P04275 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>3ZQK_1 VON WILLEBRAND FACTOR (chains A, B, C)
GSVGPGLLGVSTLGPKRNSMVLDVAFVLEGSDKIGEADFNRSKEFMEEVIQRMDVGQDSI
HVTVLQYSYMVTVEYPFSEAQSKGDILQRLREIRYQGGNRTNTGLALRYLSDHSFLVSQG
DREQAPNLVYMVTGNPASDEIKRLPGDIQVVPIGVGPNANVQELERIGWPNAPILIQDFE
TLPREAPDLVLQRCCSGEG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
CA	Calcium ion	Ca	3

Water and common crystallization additives (GOL) are not listed.

Primary citation

Calcium Modulates Force Sensing by the Von Willebrand Factor A2 Domain. Jakobi, A.J., Mashaghi, A., Tans, S.J. et al. Nat Commun (2011) 2:385. DOI 10.1038/NCOMMS1385 · 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…
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…
1FE8 2.03 Å, Crystal structure of the von willebrand factor A3 domain in complex with a FAB fragment…

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