1OAK: Von willebrand factor (VWF) A1 domain

Crystal structure of the von willebrand factor (VWF) A1 domain in complex with the function blocking nmc-4 FAB. Determined by X-ray diffraction at 2.2 Å resolution. Released 21 Oct 1998.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 5,240
Mol. weight: 69.79 kDa
Released: 21 Oct 1998

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

Secondary structure: helices and β-sheets

1OAK contains 24 α-helices and 58 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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	509	1	13
β-strand	513-520	8	14
β-strand	522	1	15
α-helix	527-542	16
β-strand	544	1	13
β-strand	546	1	14
β-strand	551-558	8	14
β-strand	562-566	5	14
α-helix	574-582	9
α-helix	584-586	3
β-strand	589	1	15
α-helix	594-600	7
α-helix	601-605	5
β-strand	615-622	8	14
α-helix	628-631	4
α-helix	634-643	10
β-strand	646-653	8	14
α-helix	659-668	10
β-strand	675-677	3	14
α-helix	680-696	17

Chain H: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	217-221	5	6
β-strand	225-226	2	7
β-strand	232-239	8	6
β-strand	247-253	7	8
β-strand	260-265	6	8
β-strand	271-273	3	8
α-helix	275-277	3
β-strand	281-286	6	6
α-helix	287-289	3
β-strand	291-296	6	6
α-helix	301-303	3
β-strand	305-312	8	8
β-strand	315	1	9
β-strand	320	1	9
β-strand	325-326	2	8
β-strand	330-332	3	8
β-strand	333-334	2	7
β-strand	340	1	10
β-strand	343-347	5	11
β-strand	358-368	11	11
β-strand	369	1	10
β-strand	374-377	4	12
α-helix	378-380	3
β-strand	382	1	12
β-strand	386-388	3	11
α-helix	389-391	3
β-strand	392-393	2	11
β-strand	398-407	10	11
α-helix	408-410	3
β-strand	417-422	6	12
α-helix	423-425	3
β-strand	427-432	6	12

Chain L: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-5	2	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	44-49	6	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	99	1	1
β-strand	102-106	5	2
β-strand	111	1	3
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-155	3	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-197	7	5
β-strand	205-210	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nmc-4 IgG1	L	protein	212	Mus musculus	P01837 (AlphaFold model)
Nmc-4 IgG1	H	protein	223	Mus musculus	P01868 (AlphaFold model)
Von willebrand factor	A	protein	196	Homo sapiens	P04275 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1OAK_1 NMC-4 IGG1 (chains L)
DIQMTQSPSSLSASLGDRVTISCSASQDINKYLNWYQQKPDGAVKLLIFYTSSLHSGVPS
RFSGSGSGTDYSLTISNLEPEDIATYYCQQYEKLPWTFGGGTKLEVKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 2 (H), FASTA

>1OAK_2 NMC-4 IGG1 (chains H)
QVQLAESGPGLVAPSQSLSITCTVSGFSLTDYGVDWVRQPPGKGLEWLGMIWGDGSTDYN
SALKSRLSITKDNSKSQVFLKMNSLQTDDTARYYCVRDPADYGNYDYALDYWGQGTSVTV
SSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD

Sequence of entity 3 (A), FASTA

>1OAK_3 VON WILLEBRAND FACTOR (chains A)
MYCSRLLDLVFLLDGSSRLSEAEFEVLKAFVVDMMERLRISQKWVRVAVVEYHDGSHAYI
GLKDRKRPSELRRIASQVKYAGSQVASTSEVLKYTLFQIFSKIDRPEASRIALLLMASQE
PQRMSRNFVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIEKQAPENKAFVLSSVDELEQQ
RDEIVSYLCDLAPEAP

Primary citation

Crystal structure of the von Willebrand factor A1 domain in complex with the function blocking NMC-4 Fab. Celikel, R., Varughese, K.I., Madhusudan et al. Nat Struct Biol (1998) 5:189-194. DOI 10.1038/nsb0398-189 · PubMed

Other PDB entries of the same protein (UniProt P01837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3D9A 1.2 Å, High Resolution Crystal Structure Structure of HyHel10 Fab Complexed to Hen Egg Lysozyme
1RUR 1.5 Å, Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set…
2AJU 1.5 Å, Cyrstal structure of cocaine catalytic antibody 7A1 Fab'
2AJV 1.5 Å, Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with Cocaine
2W60 1.5 Å, Anti citrullinated Collagen type 2 antibody acc4
2W9D 1.57 Å, Structure of Fab fragment of the ICSM 18 - anti-Prp therapeutic antibody at 1.57 A…
3BKJ 1.59 Å, Crystal structure of Fab wo2 bound to the n terminal domain of amyloid beta peptide (1-16)
3BAE 1.59 Å, Crystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28)
2R1Y 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
2R2B 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
3BKM 1.6 Å, Structure of anti-amyloid-beta Fab WO2 (Form A, P212121)
3CFB 1.6 Å, High-resolution structure of blue fluorescent antibody EP2-19G2 in complex with stilbene…

Browse structure collections

About this viewer

MolViewer shows 1OAK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.