4WK4: Metal Ion and Ligand Binding of Integrin

Metal Ion and Ligand Binding of Integrin. Determined by X-ray diffraction at 2.5 Å resolution. Released 3 Dec 2014.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,427
Mol. weight: 104.62 kDa
Ligands: CA, NAG, MG
Released: 3 Dec 2014

Explore 4WK4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WK4 contains 33 α-helices and 67 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, 41 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	1
β-strand	22-26	5	2
β-strand	34-39	6	2
β-strand	54-59	6	2
β-strand	68-70	3	2
α-helix	77-78	2
β-strand	79	1	3
α-helix	80	1
α-helix	81-83	3
β-strand	92	1	3
β-strand	94-95	2	4
β-strand	104-108	5	5
β-strand	111-116	6	5
β-strand	120-121	2	4
β-strand	130	1	4
β-strand	134-139	6	5
β-strand	144-148	5	5
β-strand	169-172	4	6
β-strand	178-182	5	6
α-helix	185-188	4
β-strand	190	1	7
β-strand	191-195	5	6
α-helix	197-201	5
β-strand	217-218	2	6
α-helix	219-221	3
α-helix	224-226	3
β-strand	231	1	7
β-strand	235-238	4	8
β-strand	247-252	6	8
β-strand	261-265	5	8
β-strand	272-277	6	8
β-strand	288-292	5	9
β-strand	301-306	6	9
β-strand	310-312	3	10
β-strand	318-320	3	10
β-strand	322	1	11
β-strand	323-327	5	9
β-strand	329	1	12
β-strand	334	1	12
β-strand	340-343	4	9
β-strand	351	1	11
β-strand	354-359	6	13
β-strand	368-373	6	13
β-strand	383-387	5	13
β-strand	400-402	3	13
α-helix	407-408	2
β-strand	419-423	5	1
β-strand	432-437	6	1
α-helix	438-440	3
β-strand	442-446	5	1

Chain B: 24 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	15-20	6
β-strand	25-28	4	14
β-strand	44-46	3	14
α-helix	47-53	7
α-helix	57-59	3
β-strand	60-61	2	14
β-strand	67-71	5	15
α-helix	73-76	4
β-strand	94-95	2	16
β-strand	98-104	7	15
β-strand	108-116	9	16
β-strand	123-130	8	17
α-helix	133-135	3
α-helix	136-139	4
α-helix	142-144	3
α-helix	145-153	9
β-strand	160-167	8	17
α-helix	180-184	5
α-helix	193-196	4
β-strand	199-206	8	17
α-helix	209-216	8
α-helix	219-221	3
β-strand	229	1	18
α-helix	231-240	10
α-helix	242-245	4
β-strand	251-258	8	17
β-strand	262	1	18
α-helix	267-271	5
α-helix	276-277	2
β-strand	283-284	2	17
β-strand	287-288	2	17
α-helix	295-298	4
α-helix	299-308	10
β-strand	312-317	6	17
α-helix	319-321	3
α-helix	322-331	10
β-strand	335-339	5	17
α-helix	347-359	13
β-strand	362-363	2	19
β-strand	364-366	3	15
β-strand	374-380	7	16
α-helix	382-384	3
α-helix	391-393	3
β-strand	394-395	2	19
β-strand	403-411	9	16
β-strand	421-427	7	15
β-strand	434-441	8	15

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	20
β-strand	7	1	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-5	A	protein	450	Homo sapiens	P08648 (AlphaFold model)
Integrin beta-1	B	protein	445	Homo sapiens	P05556 (AlphaFold model)
Ala-cys-arg-gly-asp-gly-trp-cys	C	protein	8	Homo sapiens

Sequence of entity 1 (A), FASTA

>4WK4_1 Integrin alpha-5 (chains A)
FNLDAEAPAVLSGPPGSFFGFSVEFYRPGTDGVSVLVGAPKANTSQPGVLQGGAVYLCPW
GASPTQCTPIEFDSKGSRLLESSLSSSEGEEPVEYKSLQWFGATVRAHGSSILACAPLYS
WRTEKEPLSDPVGTCYLSTDNFTRILEYAPCRSDFSWAAGQGYCQGGFSAEFTKTGRVVL
GGPGSYFWQGQILSATQEQIAESYYPEYLINLVQGQLQTRQASSIYDDSYLGYSVAVGEF
SGDDTEDFVAGVPKGNLTYGYVTILNGSDIRSLYNFSGEQMASYFGYAVAATDVNGDGLD
DLLVGAPLLMDRTPDGRPQEVGRVYVYLQHPAGIEPTPTLTLTGHDEFGRFGSSLTPLGD
LDQDGYNDVAIGAPFGGETQQGVVFVFPGGPGGLGSKPSQVLQPLWAASHTPDFFGSALR
GGRDLDGNGYPDLIVGSFGVDKAVVYRGRP

Sequence of entity 2 (B), FASTA

>4WK4_2 Integrin beta-1 (chains B)
QTDENRCLKANAKSCGECIQAGPNCGWCTNSTFLQEGMPTSARCDDLEALKKKGCPPDDI
ENPRGSKDIKKNKNVTNRSKGTAEKLKPEDITQIQPQQLVLRLRSGEPQTFTLKFKRAED
YPIDLYYLMDLSYSMKDDLENVKSLGTDLMNEMRRITSDFRIGFGSFVEKTVMPYISTTP
AKLRNPCTSEQNCTTPFSYKNVLSLTNKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAV
CGSLIGWRNVTRLLVFSTDAGFHFAGDGKLGGIVLPNDGQCHLENNMYTMSHYYDYPSIA
HLVQKLSENNIQTIFAVTEEFQPVYKELKNLIPKSAVGTLSANSSNVIQLIIDAYNSLSS
EVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDS
DSFKIRPLGFTEEVEVILQYICECE

Sequence of entity 3 (C), FASTA

>4WK4_3 ALA-CYS-ARG-GLY-ASP-GLY-TRP-CYS (chains C)
ACRGDGWC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
MG	Magnesium ion	Mg	1

Primary citation

Metal ion and ligand binding of integrin alpha 5 beta 1. Xia, W., Springer, T.A. Proc Natl Acad Sci U S A (2014) 111:17863-17868. DOI 10.1073/pnas.1420645111 · PubMed

Other PDB entries of the same protein (UniProt P08648 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4WK0 1.78 Å, Metal Ion and Ligand Binding of Integrin
4WJK 1.85 Å, Metal Ion and Ligand Binding of Integrin
9HMH 1.92 Å, Crystal structure of the Calf domains of Integrin Alpha5
4WK2 2.5 Å, Metal Ion and Ligand Binding of Integrin
9B9J 2.6 Å, Integrin alpha-5 beta-1 in complex with BIIG2 Fab
9P6S 2.61 Å, Cryo-EM structure of human integrin alpha5beta1 in complex with fibronectin (FN 7-10)
9B9K 2.7 Å, Integrin alpha-5 beta-1 in complex with MINT1526A Fab
9HMI 2.87 Å, Crystal structure of the Calf domains of Integrin Alpha5 in complex with angiopoietin2…
3VI3 2.9 Å, Crystal structure of alpha5beta1 integrin headpiece (ligand-free form)
3VI4 2.9 Å, Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide
9DIA 2.97 Å, Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin candidate 2
7NWL 3.1 Å, Cryo-EM structure of human integrin alpha5beta1 (open form) in complex with fibronectin…

Browse structure collections

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