7TCT: Integrin alpha IIB beta3 complex with UR2922

Integrin alpha IIB beta3 complex with UR2922. Determined by X-ray diffraction at 2.5 Å resolution. Released 17 Aug 2022.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Mus musculus
Chains: 8
Atoms: 22,118
Mol. weight: 302.73 kDa
Ligands: CA, MG, NAG, I1F
Released: 17 Aug 2022

Explore 7TCT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TCT contains 57 α-helices and 212 β-strands across 8 chains. Residue ranges use sequence positions (label_seq_id) from RCSB, which can differ from the residue numbers in the file. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	AA1
β-strand	23-27	5	AA2
β-strand	33-39	7	AA2
β-strand	52-57	6	AA2
β-strand	76-79	4	AA3
β-strand	82-87	6	AA3
β-strand	97-100	4	AA4
β-strand	103-108	6	AA4
β-strand	112-117	6	AA3
β-strand	120-121	2	AA3
β-strand	129-133	5	AA4
β-strand	140-143	4	AA4
α-helix	151-158	8
β-strand	172-175	4	AA5
β-strand	180-185	6	AA5
α-helix	187-192	6
β-strand	194-199	6	AA5
α-helix	200-207	8
β-strand	220-221	2	AA5
α-helix	227-231	5
β-strand	239-242	4	AA6
β-strand	252-257	6	AA6
α-helix	259-264	6
β-strand	266-270	5	AA6
β-strand	276-281	6	AA6
β-strand	293-296	4	AA7
β-strand	305-310	6	AA7
β-strand	314-317	4	AA8
β-strand	321-324	4	AA8
β-strand	327-331	5	AA7
β-strand	345-348	4	AA7
β-strand	360-364	5	AA9
β-strand	373-378	6	AA9
β-strand	388-392	5	AA9
β-strand	394-395	2	AB1
β-strand	398-399	2	AB1
β-strand	405-408	4	AA9
β-strand	420-425	6	AA1
β-strand	434-439	6	AA1
α-helix	440-442	3
β-strand	444-448	5	AA1

Chain B: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	12-18	7
β-strand	24-26	3	AB2
β-strand	38-39	2	AB2
α-helix	40-47	8
α-helix	50-52	3
β-strand	54-55	2	AB2
β-strand	60-65	6	AB3
β-strand	83-84	2	AB4
β-strand	87-92	6	AB3
β-strand	97-105	9	AB4
β-strand	112-119	8	AB5
α-helix	121-123	3
α-helix	124-130	7
α-helix	133-143	11
β-strand	149-156	8	AB5
α-helix	169-175	7
β-strand	190-197	8	AB5
α-helix	199-210	12
α-helix	221-232	12
α-helix	232-237	6
β-strand	243-250	8	AB5
α-helix	258-264	7
α-helix	291-303	13
β-strand	305-311	7	AB5
α-helix	314-325	12
β-strand	329-333	5	AB5
α-helix	339-352	14
β-strand	355-360	6	AB3
β-strand	366-374	9	AB4
β-strand	378-381	4	AB4
β-strand	385-386	2	AB3
β-strand	394-403	10	AB4
β-strand	411-418	8	AB3
β-strand	425-431	7	AB3
α-helix	437-441	5
β-strand	453-456	4	AB6
β-strand	459-462	4	AB6

Chain C: 6 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	AB7
β-strand	23-27	5	AB8
β-strand	33-39	7	AB8
β-strand	52-56	5	AB8
β-strand	76-79	4	AB9
β-strand	82-87	6	AB9
β-strand	97-100	4	AC1
β-strand	103-108	6	AC1
β-strand	112-117	6	AB9
β-strand	120-121	2	AB9
β-strand	129-134	6	AC1
β-strand	139-143	5	AC1
α-helix	151-158	8
β-strand	172-175	4	AC2
β-strand	180-185	6	AC2
α-helix	187-192	6
β-strand	194-199	6	AC2
α-helix	200-207	8
β-strand	220-221	2	AC2
α-helix	227-231	5
β-strand	239-242	4	AC3
β-strand	252-257	6	AC3
α-helix	259-264	6
β-strand	266-270	5	AC3
β-strand	276-281	6	AC3
β-strand	293-296	4	AC4
β-strand	305-310	6	AC4
β-strand	314-317	4	AC5
β-strand	321-324	4	AC5
β-strand	327-331	5	AC4
β-strand	345-348	4	AC4
β-strand	360-364	5	AC6
β-strand	373-378	6	AC6
β-strand	388-392	5	AC6
β-strand	394-395	2	AC7
β-strand	398-399	2	AC7
β-strand	405-408	4	AC6
β-strand	420-425	6	AB7
β-strand	434-439	6	AB7
α-helix	440-442	3
β-strand	444-448	5	AB7

Chain D: 17 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	12-18	7
β-strand	24-26	3	AC8
β-strand	38-39	2	AC8
α-helix	40-47	8
α-helix	50-52	3
β-strand	54-55	2	AC8
β-strand	60-65	6	AC9
α-helix	76-80	5
β-strand	83-84	2	AD1
β-strand	87-92	6	AC9
β-strand	97-105	9	AD1
β-strand	112-119	8	AD2
α-helix	121-123	3
α-helix	124-131	8
α-helix	133-143	11
β-strand	149-156	8	AD2
α-helix	169-175	7
β-strand	190-197	8	AD2
α-helix	200-209	10
α-helix	221-232	12
α-helix	232-237	6
β-strand	243-250	8	AD2
α-helix	258-264	7
α-helix	291-302	12
β-strand	305-310	6	AD2
α-helix	314-325	12
β-strand	329-332	4	AD2
α-helix	339-352	14
β-strand	355-360	6	AC9
β-strand	366-373	8	AD1
β-strand	379-381	3	AD1
β-strand	385-386	2	AC9
β-strand	394-403	10	AD1
β-strand	411-418	8	AC9
β-strand	425-431	7	AC9
α-helix	435-441	7
β-strand	453-456	4	AD3
β-strand	459-462	4	AD3

Chain E: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	AD4
β-strand	10-12	3	AD5
β-strand	10-12	3	AD6
β-strand	18-25	8	AD4
α-helix	28-32	5
β-strand	34-40	7	AD5
β-strand	44-51	8	AD5
β-strand	58-60	3	AD5
α-helix	62-65	4
β-strand	68-73	6	AD4
β-strand	78-83	6	AD4
α-helix	87-91	5
β-strand	92-98	7	AD5
β-strand	92-98	7	AD6
β-strand	108-109	2	AD6
β-strand	113-117	5	AD5
β-strand	113-117	5	AD6
β-strand	126-130	5	AD7
β-strand	126-130	5	AD8
β-strand	141-151	11	AD7
β-strand	141-151	11	AD8
β-strand	157-160	4	AD9
β-strand	169-171	3	AD7
β-strand	175-176	2	AD8
β-strand	181-190	10	AD7
β-strand	181-190	10	AD8
β-strand	200-205	6	AD9
β-strand	210-215	6	AD9

Chain F: 3 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	AE1
β-strand	10-13	4	AE2
β-strand	10-13	4	AE3
β-strand	19-25	7	AE1
β-strand	33-38	6	AE2
β-strand	44-49	6	AE2
β-strand	53-54	2	AE2
β-strand	62-67	6	AE1
β-strand	70-75	6	AE1
α-helix	79-83	5
β-strand	85-90	6	AE2
β-strand	85-90	6	AE3
β-strand	97-98	2	AE3
β-strand	102-106	5	AE2
β-strand	102-106	5	AE3
β-strand	114-118	5	AE4
α-helix	121-126	6
β-strand	129-139	11	AE4
β-strand	145-150	6	AE5
β-strand	145-150	6	AE6
β-strand	153-155	3	AE5
β-strand	153-155	3	AE6
β-strand	159-163	5	AE4
β-strand	173-182	10	AE4
α-helix	183-187	5
β-strand	191-198	8	AE5
β-strand	191-198	8	AE6
β-strand	201-205	5	AE5
β-strand	208-210	3	AE6

Chain H: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	AE7
β-strand	10-12	3	AE8
β-strand	10-12	3	AE9
β-strand	18-25	8	AE7
α-helix	28-32	5
β-strand	34-40	7	AE8
β-strand	44-51	8	AE8
β-strand	58-60	3	AE8
α-helix	62-65	4
β-strand	68-73	6	AE7
β-strand	78-83	6	AE7
α-helix	87-91	5
β-strand	92-98	7	AE8
β-strand	92-98	7	AE9
β-strand	108-109	2	AE9
β-strand	113-117	5	AE8
β-strand	113-117	5	AE9
β-strand	126-130	5	AF1
β-strand	126-130	5	AF2
β-strand	141-151	11	AF1
β-strand	141-151	11	AF2
β-strand	157-160	4	AF3
β-strand	169-171	3	AF1
β-strand	175-177	3	AF2
β-strand	180-190	11	AF1
β-strand	180-190	11	AF2
β-strand	200-205	6	AF3
β-strand	210-215	6	AF3

Chain L: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	AF4
β-strand	10-13	4	AF5
β-strand	10-13	4	AF6
β-strand	19-25	7	AF4
β-strand	33-38	6	AF5
β-strand	45-49	5	AF5
β-strand	53-54	2	AF5
β-strand	62-67	6	AF4
β-strand	70-75	6	AF4
α-helix	79-83	5
β-strand	85-90	6	AF5
β-strand	85-90	6	AF6
β-strand	97-98	2	AF6
β-strand	102-106	5	AF5
β-strand	102-106	5	AF6
β-strand	114-118	5	AF7
α-helix	121-127	7
β-strand	129-139	11	AF7
β-strand	145-150	6	AF8
β-strand	153-155	3	AF8
β-strand	159-163	5	AF7
β-strand	173-182	10	AF7
α-helix	183-187	5
β-strand	191-198	8	AF8
β-strand	201-210	10	AF8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-IIb heavy chain	A, C	protein	457	Homo sapiens	P08514 (AlphaFold model)
Isoform Beta-3C of Integrin beta-3	B, D	protein	472	Homo sapiens	P05106 (AlphaFold model)
Fab heavy chain	E, H	protein	221	Mus musculus
Fab light chain	F, L	protein	214	Mus musculus

Sequence of entity 1 (A, C), FASTA

>7TCT_1 Integrin alpha-IIb heavy chain (chains A, C)
LNLDPVQLTFYAGPNGSQFGFSLDFHKDSHGRVAIVVGAPRTLGPSQEETGGVFLCPWRA
EGGQCPSLLFDLRDETRNVGSQTLQTFKARQGLGASVVSWSDVIVACAPWQHWNVLEKTE
EAEKTPVGSCFLAQPESGRRAEYSPCRGNTLSRIYVENDFSWDKRYCEAGFSSVVTQAGE
LVLGAPGGYYFLGLLAQAPVADIFSSYRPGILLWHVSSQSLSFDSSNPEYFDGYWGYSVA
VGEFDGDLNTTEYVVGAPTWSWTLGAVEILDSYYQRLHRLRGEQMASYFGHSVAVTDVNG
DGRHDLLVGAPLYMESRADRKLAEVGRVYLFLQPRGPHALGAPSLLLTGTQLYGRFGSAI
APLGDLDRDGYNDIAVAAPYGGPSGRGQVLVFLGQSEGLRSRPSQVLDSPFPTGSAFGFS
LRGAVDIDDNGYPDLIVGAYGANQVAVYRAQPVVKAS

Sequence of entity 2 (B, D), FASTA

>7TCT_2 Isoform Beta-3C of Integrin beta-3 (chains B, D)
GPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEFPVSE
ARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDYPVDIYYLMDL
SYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDM
KTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRN
DASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLS
QKNINLIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRSKVELEVR
DLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVG
FKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGTFECGVCRCGPGWLGSQCE

Sequence of entity 3 (E, H), FASTA

>7TCT_3 Fab heavy chain (chains E, H)
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYVHWVKQRPEQGLEWIGRIDPANGYTKY
DPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCVRPLYDYYAMDYWGQGTSVTVSSA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGP

Sequence of entity 4 (F, L), FASTA

>7TCT_4 Fab light chain (chains F, L)
DILMTQSPSSMSVSLGDTVSITCHASQGISSNIGWLQQKPGKSFMGLIYYGTNLVDGVPS
RFSGSGSGADYSLTISSLDSEDFADYYCVQYAQLPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	12
MG	Magnesium ion	Mg	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
I1F	{5-[N-(4-carbamimidoylbenzoyl)-4-nitro-L-phenylalanyl]-4,5,6,7-tetrahydro-2H-py…	C25 H25 N7 O6	2

Water and common crystallization additives (CL, SO4) are not listed.

Primary citation

A general chemical principle for creating closure-stabilizing integrin inhibitors. Lin, F.Y., Li, J., Xie, Y. et al. Cell (2022) 185:3533-3550.e27. DOI 10.1016/j.cell.2022.08.008 · PubMed

Other PDB entries of the same protein (UniProt P08514 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SC4 1.85 Å, filamin complex-1
7UDH 2.0 Å, Integrin alpha IIB beta3 complex with BMS4-3
7UBR 2.05 Å, Integrin alpha IIB beta3 complex with GR144053
3T3P 2.2 Å, A Novel High Affinity Integrin alphaIIbbeta3 Receptor Antagonist That Unexpectedly…
7TMZ 2.2 Å, Integrin alpha IIB beta3 complex with BMS compound 4
3NIG 2.25 Å, The Closed Headpiece of Integrin IIb 3 and its Complex with an IIb 3 -Specific…
7U9V 2.25 Å, Integrin alpha IIB beta3 complex with BMS4-1
3NID 2.3 Å, The Closed Headpiece of Integrin alphaIIB beta3 and its Complex with an alpahIIB beta3…
7L8P 2.35 Å, Integrin alphaIIbbeta3 in complex with sibrafiban
7UCY 2.35 Å, Integrin alpha IIB beta3 complex with gantofiban
3ZE2 2.35 Å, Integrin alphaIIB beta3 headpiece and RGD peptide complex
7UKT 2.37 Å, Integrin alpha IIB beta3 complex with BMS4.2

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