2V5O: Human IGF2R domains 11-14

Structure of human IGF2R domains 11-14. Determined by X-ray diffraction at 2.91 Å resolution. Released 11 Dec 2007.

Method: X-ray diffraction
Resolution: 2.91 Å
Organism: Homo sapiens
Chains: 1
Atoms: 4,686
Mol. weight: 70.07 kDa
Ligands: NAG
Released: 11 Dec 2007

Explore 2V5O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2V5O contains 23 α-helices and 68 β-strands across 1 chain. 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: 23 helices, 68 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
β-strand	1565-1567	3	2
β-strand	1573-1575	3	2
β-strand	1576	1	3
β-strand	1581-1584	4	4
β-strand	1587-1592	6	4
β-strand	1593	1	3
β-strand	1597	1	5
α-helix	1604	1
β-strand	1605	1	5
α-helix	1606	1
β-strand	1607-1614	8	4
β-strand	1625-1630	6	4
β-strand	1635-1642	8	4
α-helix	1643-1645	3
β-strand	1653-1656	4	6
β-strand	1659-1662	4	6
α-helix	1664-1666	3
β-strand	1673-1675	3	7
α-helix	1676	1
β-strand	1690-1692	3	7
α-helix	1697-1700	4
α-helix	1706-1707	2
β-strand	1712-1714	3	7
α-helix	1720-1721	2
β-strand	1722-1725	4	7
β-strand	1726-1727	2	8
β-strand	1732-1733	2	8
β-strand	1740-1741	2	8
β-strand	1743-1745	3	8
α-helix	1749-1750	2
β-strand	1759-1766	8	8
β-strand	1775-1777	3	8
β-strand	1784-1791	8	8
α-helix	1792-1794	3
α-helix	1796-1797	2
β-strand	1805-1807	3	9
β-strand	1814-1816	3	9
α-helix	1818-1821	4
β-strand	1825-1829	5	10
β-strand	1832-1836	5	10
β-strand	1853	1	11
β-strand	1855-1858	4	10
β-strand	1863-1865	3	10
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
α-helix	1947	1
β-strand	1948	1	12
α-helix	1949	1
β-strand	1950-1957	8	11
β-strand	1967-1972	6	11
β-strand	1976-1983	8	11
β-strand	1991	1	16
β-strand	1995-1997	3	17
β-strand	2002-2004	3	17
α-helix	2005-2007	3
β-strand	2015-2019	5	18
β-strand	2022-2026	5	18
β-strand	2030	1	16
α-helix	2035-2036	2
β-strand	2037	1	19
β-strand	2039	1	19
β-strand	2043-2048	6	18
β-strand	2054-2059	6	18
α-helix	2060-2062	3
β-strand	2064-2068	5	20
β-strand	2071-2076	6	20
β-strand	2081	1	21
β-strand	2087	1	21
β-strand	2089-2096	8	20
β-strand	2100-2109	10	20
β-strand	2114-2121	8	20
α-helix	2122-2124	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cation-independent mannose-6-phosphate receptor	A	protein	627	Homo sapiens	P11717 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2V5O_1 CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR (chains A)
MKSNEHDDCQVTNPSTGHLFDLSSLSGRAGFTAAYSEKGLVYMSICGENENCPPGVGACF
GQTRISVGKANKRLRYVDQVLQLVYKDGSPCPSKSGLSYKSVISFVCRPEAGPTNRPMLI
SLDKQTCTLFFSWHTPLACEQATECSVRNGSSIVDLSPLIHRTGGYEAYDESEDDASDTN
PDFYINICQPLNPMHAVPCPAGAAVCKVPIDGPPIDIGRVAGPPILNPIANEIYLNFESS
TPCLADKHFNYTSLIAFHCKRGVSMGTPKLLRTSECDFVFEWETPVVCPDEVRMDGCTLT
DEQLLYSFNLSSLSTSTFKVTRDSRTYSVGVCTFAVGPEQGGCKDGGVCLLSGTKGASFG
RLQSMKLDYRHQDEAVVLSYVNGDRCPPETDDGVPCVFPFIFNGKSYEECIIESRAKLWC
STTADYDRDHEWGFCRHSNSYRTSSIIFKCDEDEDIGRPQVFSEVRGCDVTFEWKTKVVC
PPKKLECKFVQKHKTYDLRLLSSLTGSWSLVHNGVSYYINLCQKIYKGPLGCSERASICR
RTTTGDVQVLGLVHTQKLGVIGDKVVVTYSKGYPCGGNKTASSVIELTCTKTVGRPAFKR
FDIDSCTYYFSWDSRAACAVKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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

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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