2V5P: Complex structure of human IGF2R domains 11-13

Complex structure of human IGF2R domains 11-13 bound to igf-II. Determined by X-ray diffraction at 4.1 Å resolution. Released 11 Dec 2007.

Method: X-ray diffraction
Resolution: 4.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,989
Mol. weight: 125.49 kDa
Ligands: NAG
Released: 11 Dec 2007

Explore 2V5P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2V5P contains 42 α-helices and 111 β-strands across 4 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: 15 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	1517-1519	3	1
β-strand	1526-1528	3	1
α-helix	1530-1532	3
β-strand	1538-1542	5	2
β-strand	1546-1550	5	2
α-helix	1560	1
β-strand	1563	1	3
β-strand	1565	1	2
β-strand	1576	1	3
β-strand	1581-1584	4	2
β-strand	1587-1592	6	2
β-strand	1593	1	3
β-strand	1597	1	4
α-helix	1598	1
β-strand	1605	1	4
β-strand	1607-1614	8	2
β-strand	1625-1630	6	2
β-strand	1635-1642	8	2
α-helix	1643-1645	3
β-strand	1653-1656	4	5
β-strand	1659-1662	4	5
α-helix	1664-1666	3
β-strand	1673-1674	2	6
α-helix	1675-1676	2
β-strand	1690-1692	3	6
α-helix	1697-1700	4
β-strand	1712-1714	3	6
β-strand	1722-1725	4	6
β-strand	1726-1727	2	7
α-helix	1731	1
β-strand	1732-1733	2	7
β-strand	1740-1745	6	7
β-strand	1760-1766	7	7
β-strand	1776-1779	4	7
β-strand	1786-1791	6	7
α-helix	1792-1794	3
α-helix	1798-1800	3
β-strand	1805-1807	3	8
β-strand	1814-1816	3	8
α-helix	1817-1819	3
β-strand	1825	1	9
β-strand	1828-1829	2	10
β-strand	1832-1833	2	10
β-strand	1834-1836	3	9
β-strand	1853	1	11
β-strand	1855-1857	3	9
β-strand	1864-1865	2	9
β-strand	1868-1877	10	11
β-strand	1882-1888	7	11
β-strand	1892	1	12
α-helix	1893-1895	3
β-strand	1896-1897	2	13
α-helix	1901	1
β-strand	1902	1	13
α-helix	1903	1
β-strand	1907-1909	3	14
β-strand	1912-1914	3	14
β-strand	1918	1	15
β-strand	1926-1928	3	15
β-strand	1932	1	14
α-helix	1933-1936	4
β-strand	1939-1941	3	15
β-strand	1942-1943	2	13
β-strand	1948	1	12
β-strand	1950-1957	8	11
β-strand	1966-1972	7	11
β-strand	1976-1983	8	11

Chain B: 17 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	1517-1519	3	16
α-helix	1525	1
β-strand	1526-1528	3	16
α-helix	1530-1532	3
β-strand	1538-1542	5	17
β-strand	1546-1550	5	17
α-helix	1560	1
β-strand	1563	1	18
β-strand	1565	1	17
β-strand	1576	1	18
β-strand	1581-1583	3	19
β-strand	1588-1592	5	19
β-strand	1593	1	18
β-strand	1597	1	20
α-helix	1604	1
β-strand	1605	1	20
α-helix	1606	1
β-strand	1607-1614	8	19
β-strand	1625-1630	6	19
β-strand	1635-1642	8	19
α-helix	1643-1645	3
β-strand	1653-1656	4	21
β-strand	1659-1662	4	21
α-helix	1664-1666	3
β-strand	1673-1674	2	22
α-helix	1675-1676	2
β-strand	1690-1692	3	22
α-helix	1697-1699	3
β-strand	1712-1714	3	22
α-helix	1720-1721	2
β-strand	1722-1725	4	22
β-strand	1726-1727	2	23
α-helix	1731	1
β-strand	1732-1733	2	23
β-strand	1740-1745	6	23
β-strand	1759-1766	8	23
β-strand	1776-1779	4	23
β-strand	1784-1791	8	23
α-helix	1792-1794	3
α-helix	1796-1800	5
β-strand	1805-1807	3	24
β-strand	1814-1816	3	24
β-strand	1828-1829	2	25
β-strand	1832-1833	2	25
β-strand	1836	1	26
β-strand	1853	1	27
β-strand	1855	1	26
β-strand	1856-1857	2	28
β-strand	1858	1	25
β-strand	1864-1865	2	28
β-strand	1868-1877	10	27
β-strand	1882-1888	7	27
β-strand	1892	1	29
α-helix	1893-1895	3
β-strand	1896-1897	2	30
α-helix	1901	1
β-strand	1902	1	30
α-helix	1903	1
β-strand	1907-1909	3	31
β-strand	1912-1914	3	31
β-strand	1918	1	32
β-strand	1926-1928	3	32
β-strand	1932	1	31
α-helix	1933-1936	4
β-strand	1939-1941	3	32
β-strand	1942-1943	2	30
β-strand	1948	1	29
β-strand	1950-1955	6	27
β-strand	1956-1957	2	33
β-strand	1966-1973	8	27
β-strand	1976-1981	6	27
β-strand	1982-1983	2	33

Chain C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	26	1	34
α-helix	42-46	5
α-helix	54-57	4
β-strand	60	1	34
α-helix	61-62	2

Chain D: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	22-24	3
β-strand	26	1	35
α-helix	42	1
α-helix	43-47	5
α-helix	54-57	4
β-strand	60	1	35
α-helix	61-62	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cation-independent mannose-6-phosphate receptor	A, B	protein	492	Homo sapiens	P11717 (AlphaFold model)
Insulin-like growth factor II	C, D	protein	67	Homo sapiens	P01344 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2V5P_1 CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR (chains A, B)
MKSNEHDDCQVTNPSTGHLFDLSSLSGRAGFTAAYSEKGLVYMSICGENENCPPGVGACF
GQTRISVGKANKRLRYVDQVLQLVYKDGSPCPSKSGLSYKSVISFVCRPEAGPTNRPMLI
SLDKQTCTLFFSWHTPLACEQATECSVRNGSSIVDLSPLIHRTGGYEAYDESEDDASDTN
PDFYINICQPLNPMHAVPCPAGAAVCKVPIDGPPIDIGRVAGPPILNPIANEIYLNFESS
TPCLADKHFNYTSLIAFHCKRGVSMGTPKLLRTSECDFVFEWETPVVCPDEVRMDGCTLT
DEQLLYSFNLSSLSTSTFKVTRDSRTYSVGVCTFAVGPEQGGCKDGGVCLLSGTKGASFG
RLQSMKLDYRHQDEAVVLSYVNGDRCPPETDDGVPCVFPFIFNGKSYEECIIESRAKLWC
STTADYDRDHEWGFCRHSNSYRTSSIIFKCDEDEDIGRPQVFSEVRGCDVTFEWKTKVVC
PPKKLKHHHHHH

Sequence of entity 2 (C, D), FASTA

>2V5P_2 INSULIN-LIKE GROWTH FACTOR II (chains C, D)
AYRPSETLCGGELVDTLQFVCGDRGFYFSRPASRVSRRSRGIVEECCFRSCDLALLETYC
ATPAKSE

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Structure and Functional Analysis of the Igf-II/Igf2R Interaction. Brown, J., Delaine, C., Zaccheo, O.J. et al. EMBO J (2008) 27:265. DOI 10.1038/SJ.EMBOJ.7601938 · PubMed

Other PDB entries of the same protein (UniProt P11717 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GP0 1.4 Å, Human IGF2R domain 11
6Z30 1.5 Å, Human cation-independent mannose 6-phosphate/ IGF2 receptor domains 9-10
1E6F 1.75 Å, Human MIR-receptor, repeat 11
1GQB 1.8 Å, Human mir-receptor, repeat 11
1GP3 1.95 Å, Human IGF2R domain 11
1JWG 2.0 Å, VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide
6N5X 2.05 Å, Crystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121…
6N5Y 2.26 Å, Crystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121…
1LF8 2.3 Å, Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide
1JPL 2.4 Å, GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose…
6V02 2.46 Å, N-terminal 5 domains of CI-MPR
6P8I 2.54 Å, N-terminal 5 domains of IGFIIR

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