1FE8: Von willebrand factor A3 domain

Crystal structure of the von willebrand factor A3 domain in complex with a FAB fragment of IgG RU5 that inhibits collagen binding. Determined by X-ray diffraction at 2.03 Å resolution. Released 4 Apr 2001.

Method: X-ray diffraction
Resolution: 2.03 Å
Organisms: Homo sapiens, Mus musculus
Chains: 9
Atoms: 14,872
Mol. weight: 201.59 kDa
Ligands: NAG, CAC
Released: 4 Apr 2001

Explore 1FE8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1FE8 contains 71 α-helices and 153 β-strands across 9 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	942-957	16
β-strand	960	1	1
β-strand	965-972	8	1
β-strand	977-980	4	1
α-helix	988-996	9
α-helix	1007-1018	12
α-helix	1021-1023	3
α-helix	1025-1026	2
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

Chain B: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	927-934	8	13
α-helix	942-957	16
β-strand	960	1	13
β-strand	965-972	8	13
β-strand	977-980	4	13
α-helix	988-996	9
α-helix	1007-1017	11
α-helix	1021-1023	3
α-helix	1025-1026	2
β-strand	1030-1037	8	13
α-helix	1046-1054	9
β-strand	1057-1064	8	13
α-helix	1070-1076	7
α-helix	1078-1084	7
β-strand	1086-1088	3	13
α-helix	1093-1099	7
α-helix	1105-1108	4

Chain C: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	927-934	8	24
α-helix	941-957	17
β-strand	960	1	24
β-strand	965-972	8	24
β-strand	977-980	4	24
α-helix	988-996	9
α-helix	1007-1018	12
α-helix	1021-1023	3
α-helix	1025-1026	2
β-strand	1030-1037	8	24
α-helix	1046-1054	9
β-strand	1057-1064	8	24
α-helix	1070-1077	8
α-helix	1078-1080	3
β-strand	1086-1088	3	24
α-helix	1091-1093	3
α-helix	1096-1099	4
α-helix	1105-1108	4

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	2
β-strand	11-12	2	3
β-strand	18-25	8	2
β-strand	33-39	7	4
β-strand	46-51	6	4
β-strand	57-59	3	4
α-helix	61-63	3
β-strand	67-72	6	2
β-strand	77-82	6	2
α-helix	87-89	3
β-strand	91-98	8	4
β-strand	104-105	2	4
β-strand	109-111	3	4
β-strand	112-113	2	3
α-helix	116-118	3
β-strand	119	1	5
α-helix	120-121	2
β-strand	122-126	5	6
β-strand	137-147	11	6
β-strand	148	1	5
β-strand	153-156	4	7
α-helix	157-159	3
β-strand	161	1	7
β-strand	165-167	3	6
α-helix	168-170	3
β-strand	171-173	3	6
β-strand	176-186	11	6
α-helix	187-189	3
β-strand	196-201	6	7
α-helix	202-204	3
β-strand	206-211	6	7

Chain I: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	11-12	2	15
β-strand	18-25	8	14
β-strand	33-39	7	16
β-strand	46-51	6	16
β-strand	57-59	3	16
α-helix	61-63	3
β-strand	67-72	6	14
α-helix	73-75	3
β-strand	77-82	6	14
α-helix	87-89	3
β-strand	91-98	8	16
β-strand	104-105	2	16
β-strand	109-111	3	16
β-strand	112-113	2	15
α-helix	116-118	3
β-strand	119	1	17
α-helix	120-121	2
β-strand	122-126	5	18
β-strand	137-147	11	18
β-strand	148	1	17
β-strand	153-156	4	19
α-helix	157-159	3
β-strand	161	1	19
β-strand	165-167	3	18
α-helix	168-170	3
β-strand	171-173	3	18
β-strand	176-186	11	18
β-strand	196-201	6	19
α-helix	202-204	3
β-strand	206-211	6	19

Chain J: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	25
β-strand	11-12	2	26
β-strand	17-25	9	25
β-strand	33-39	7	27
β-strand	46-51	6	27
β-strand	57-59	3	27
β-strand	67-72	6	25
β-strand	77-83	7	25
β-strand	91-98	8	27
β-strand	104-105	2	27
β-strand	109-111	3	27
β-strand	112-113	2	26
β-strand	119	1	28
β-strand	122-126	5	29
β-strand	137-147	11	29
β-strand	148	1	28
β-strand	153-156	4	30
α-helix	157-159	3
β-strand	161	1	30
β-strand	165-167	3	29
α-helix	168-170	3
β-strand	171-173	3	29
β-strand	176-186	11	29
α-helix	187-189	3
β-strand	196-201	6	30
α-helix	202-204	3
β-strand	206-211	6	30

Chains L and M: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	10-13	4	9
β-strand	19-25	7	8
β-strand	33-38	6	9
β-strand	44-49	6	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	85-90	6	9
α-helix	96	1
β-strand	97-98	2	9
β-strand	102-106	5	9
β-strand	111	1	10
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-155	3	12
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-187	5
β-strand	191-197	7	12
β-strand	205-210	6	12

Chain N: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	31
β-strand	10-13	4	27
β-strand	19-25	7	31
β-strand	33-38	6	27
β-strand	44-49	6	27
β-strand	53-54	2	27
α-helix	55	1
β-strand	62-67	6	31
β-strand	70-75	6	31
α-helix	80-82	3
β-strand	85-90	6	27
α-helix	96	1
β-strand	97-98	2	27
β-strand	102-106	5	27
β-strand	111	1	32
β-strand	114-118	5	33
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	33
β-strand	140	1	32
β-strand	145-150	6	34
β-strand	153-154	2	34
β-strand	159-163	5	33
α-helix	164-167	4
β-strand	173-182	10	33
α-helix	183-187	5
β-strand	191-197	7	34
β-strand	205-210	6	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Von willebrand factor	A, B, C	protein	196	Homo sapiens	P04275 (AlphaFold model)
Immunoglobulin IgG RU5	H, I, J	protein	210	Mus musculus	P01863 (AlphaFold model)
Immunoglobulin IgG RU5	L, M, N	protein	211	Mus musculus	P01837 (AlphaFold model)

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

>1FE8_1 VON WILLEBRAND FACTOR (chains A, B, C)
GSHMAPDCSQPLDVILLLDGSSSFPASYFDEMKSFAKAFISKANIGPRLTQVSVLQYGSI
TTIDVPWNVVPEKAHLLSLVDVMQREGGPSQIGDALGFAVRYLTSEMHGARPGASKAVVI
LVTDVSVDSVDAAADAARSNRVTVFPIGIGDRYDAAQLRILAGPAGDSNVVKLQRIEDLP
TMVTLGNSFLHKLCSG

Sequence of entity 2 (H, I, J), FASTA

>1FE8_2 IMMUNOGLOBULIN IGG RU5 (chains H, I, J)
DVKLVQSGPGLVAPSQSLSITCTVSGFSLTTYGVSWVRQPPGKGLEWLGVIWGDGNTTYH
SALISRLSISKDNSRSQVFLKLNSLHTDDTATYYCAGNYYGMDYWGQGTSVTVSSAETTA
PSVYKLEPVSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVT
SSTWPSQSITCNVAHPASSTKVDKKIEPRG

Sequence of entity 3 (L, M, N), FASTA

>1FE8_3 IMMUNOGLOBULIN IGG RU5 (chains L, M, N)
DIAMTQTTSSLSASLGQKVTISCRASQDIGNYLNWYQQKPDGTVRLLIYYTSRLHSGVPS
RFSGSGSGTDYSLTISNLESEDIATYFCQNGGTNPWTFGGGTKLEVKRADAAPTTSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CAC	Cacodylate ion	C2 H6 As O2	1

Primary citation

Identification of the collagen-binding site of the von Willebrand factor A3-domain. Romijn, R.A., Bouma, B., Wuyster, W. et al. J Biol Chem (2001) 276:9985-9991. DOI 10.1074/jbc.M006548200 · 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…

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