8W30: Alpha-V beta-1 integrin headpiece

Crystal structure of alpha-V beta-1 integrin headpiece in complex with TR01225179. Determined by X-ray diffraction at 2.45 Å resolution. Released 1 Jan 2025.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,551
Mol. weight: 120.6 kDa
Ligands: A1AFA, NAG, CA
Released: 1 Jan 2025

Explore 8W30 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W30 contains 31 α-helices and 76 β-strands across 2 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: 13 helices, 54 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	22-26	5	2
β-strand	35-40	6	2
β-strand	55-60	6	2
β-strand	67-70	4	2
α-helix	77-78	2
β-strand	79-81	3	3
β-strand	84-85	2	3
β-strand	87-88	2	4
β-strand	97-101	5	5
β-strand	104-109	6	5
β-strand	113-114	2	4
β-strand	123	1	4
β-strand	127-131	5	5
β-strand	136-139	4	5
β-strand	160-163	4	6
β-strand	168-173	6	6
α-helix	176-179	4
β-strand	181	1	7
β-strand	182-187	6	6
α-helix	188-193	6
β-strand	207-209	3	6
α-helix	215-217	3
β-strand	222	1	7
β-strand	225-229	5	8
α-helix	237	1
β-strand	238-243	6	8
β-strand	252-256	5	8
β-strand	263-268	6	8
β-strand	279-283	5	9
β-strand	292-297	6	9
β-strand	301-303	3	10
β-strand	309-311	3	10
β-strand	314-320	7	9
β-strand	326-332	7	9
β-strand	344-348	5	11
β-strand	357-362	6	11
α-helix	367-369	3
β-strand	372-377	6	11
β-strand	378-379	2	12
β-strand	382-383	2	12
β-strand	389-392	4	11
α-helix	393	1
β-strand	407-412	6	1
β-strand	421-426	6	1
α-helix	427-429	3
β-strand	431-437	7	1
α-helix	438-439	2
β-strand	440-441	2	13
β-strand	443-450	8	14
β-strand	453-454	2	15
β-strand	461-462	2	16
α-helix	463	1
β-strand	469-470	2	16
β-strand	472-481	10	14
β-strand	490-499	10	17
β-strand	511-513	3	14
β-strand	520	1	17
β-strand	523-528	6	17
β-strand	535-542	8	14
α-helix	543-544	2
α-helix	545-547	3
β-strand	555-562	8	17
α-helix	566-568	3
β-strand	577-578	2	13
β-strand	586-590	5	17
β-strand	591-592	2	15

Chain B: 18 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	67-71	5	18
α-helix	73-76	4
β-strand	94-95	2	19
β-strand	98-103	6	18
β-strand	109-116	8	19
β-strand	123-130	8	20
α-helix	133-135	3
α-helix	136-140	5
α-helix	145-153	9
β-strand	160-167	8	20
α-helix	180-184	5
α-helix	193-196	4
β-strand	199-206	8	20
α-helix	209-217	9
β-strand	229	1	21
α-helix	231-240	10
α-helix	242-244	3
β-strand	251-258	8	20
β-strand	262	1	21
α-helix	267-271	5
β-strand	283-284	2	20
β-strand	287-288	2	20
α-helix	295-298	4
α-helix	299-308	10
β-strand	311-318	8	20
α-helix	319-321	3
α-helix	322-331	10
β-strand	335-340	6	20
α-helix	347-359	13
β-strand	362-363	2	22
β-strand	364-366	3	18
α-helix	368-370	3
β-strand	374-380	7	19
α-helix	382-384	3
β-strand	386-387	2	19
α-helix	389-393	5
β-strand	394-395	2	22
β-strand	403-411	9	19
β-strand	421-427	7	18
β-strand	434-440	7	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V heavy chain	A	protein	605	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-1	B	protein	456	Homo sapiens	P05556 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8W30_1 Integrin alpha-V heavy chain (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGYP
DLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLK
ADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIA
YLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLDGTGGL
EVLFQ

Sequence of entity 2 (B), FASTA

>8W30_2 Integrin beta-1 (chains B)
QTDENRCLKANAKSCGECIQAGPNCGWCTNSTFLQEGMPTSARCDDLEALKKKGCPPDDI
ENPRGSKDIKKNKNVTNRSKGTAEKLKPEDITQIQPQQLVLRLRSGEPQTFTLKFKRAED
YPIDLYYLMDLSYSMKDDLENVKSLGTDLMNEMRRITSDFRIGFGSFVEKTVMPYISTTP
AKLRNPCTSEQNCTSPFSYKNVLSLTNKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAV
CGSLIGWRNVTRLLVFSTDAGFHFAGDGKLGGIVLPNDGQCHLENNMYTMSHYYDYPSIA
HLVQKLSENNIQTIFAVTEEFQPVYKELKNLIPKSAVGTLSANSSNVIQLIIDAYNSLSS
EVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISIGDEVQFEISITSNKCPKKDS
DSFKIRPLGFTEEVEVILQYICECEDTSGLENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
A1AFA	N-(2,4-dichlorobenzoyl)-L-phenylalanine	C16 H13 Cl2 N O3	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
CA	Calcium ion	Ca	6

Primary citation

Design and Discovery of a Potent and Selective Inhibitor of Integrin alpha v beta 1. Sabat, M., Carney, D.W., Hernandez-Torres, G. et al. J Med Chem (2024) 67:10306-10320. DOI 10.1021/acs.jmedchem.4c00743 · PubMed

Other PDB entries of the same protein (UniProt P06756 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CZD 2.23 Å, Crystal structure of integrin avb6 headpiece in complex with compound 30
5FFG 2.25 Å, Crystal structure of integrin alpha V beta 6 head
9CZA 2.49 Å, Crystal structure of integrin avb6 headpiece in complex with compound 18
4UM9 2.5 Å, Crystal structure of alpha V beta 6 with peptide
9CZF 2.53 Å, Crystal structure of integrin avb6 headpiece in complex with compound MORF-627
9CZ7 2.57 Å, Crystal structure of integrin avb6 headpiece in complex with compound 12
6OM1 2.66 Å, Crystal structure of an atypical integrin
8VS6 2.73 Å, L-TGF-b3/avb8
6OM2 2.77 Å, Crystal structure of atypical integrin alphaV beta8 with proTGF-beta1 ligand peptide
9IUJ 2.78 Å, Integrin alpha-v beta-3 in complex with rhodostomin
9LT3 2.79 Å, Integrin alpha-v beta-3 in complex with Trimucrin
8XEL 2.8 Å, Cryo-EM structure of integrin ITGAV/ITGB3 complex, conformation 3

Browse structure collections

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