2VYT: Sex comb on midleg-like protein 2

The MBT repeats of human SCML2 bind to peptides containing mono methylated lysine. Determined by X-ray diffraction at 1.9 Å resolution. Released 5 Aug 2008.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 3,342
Mol. weight: 49.77 kDa
Ligands: MLZ
Released: 5 Aug 2008

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

Secondary structure: helices and β-sheets

2VYT contains 26 α-helices and 30 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: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	35-42	8
β-strand	46	1	1
α-helix	47-48	2
α-helix	49-51	3
α-helix	58-60	3
β-strand	68-73	6	2
β-strand	76-89	14	2
β-strand	92-97	6	2
β-strand	100	1	3
β-strand	106-109	4	2
β-strand	115-116	2	2
α-helix	120-123	4
β-strand	134	1	3
β-strand	136	1	4
α-helix	138-140	3
α-helix	141-149	9
β-strand	154	1	2
α-helix	155-156	2
α-helix	157-159	3
α-helix	161-167	7
β-strand	177-182	6	1
β-strand	185-198	14	1
β-strand	201-206	6	1
α-helix	211-213	3
β-strand	215-218	4	1
β-strand	224-225	2	1
α-helix	229-233	5
α-helix	236	1
β-strand	237	1	1
α-helix	238-240	3

Chain B: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	35-42	8
β-strand	46	1	5
α-helix	47-48	2
α-helix	49-51	3
α-helix	58-60	3
β-strand	68-71	4	6
β-strand	81-89	9	6
β-strand	92-97	6	6
β-strand	106-109	4	6
β-strand	115-116	2	6
α-helix	120-124	5
α-helix	153	1
β-strand	154	1	6
α-helix	155-156	2
α-helix	157-159	3
β-strand	161	1	4
α-helix	162-167	6
β-strand	177-181	5	5
β-strand	189-198	10	5
β-strand	201-206	6	5
α-helix	211-213	3
β-strand	215-218	4	5
β-strand	224-225	2	5
α-helix	229-233	5
β-strand	237	1	5
α-helix	238-241	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sex comb on midleg-like protein 2	A, B	protein	221	HOMO SAPIENS	Q9UQR0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2VYT_1 SEX COMB ON MIDLEG-LIKE PROTEIN 2 (chains A, B)
GSTSSVQRDDFHWEEYLKETGSISAPSECFRQSQIPPVNDFKVGMKLEARDPRNATSVCI
ATVIGITGARLRLRLDGSDNRNDFWRLVDSPDIQPVGTCEKEGDLLQPPLGYQMNTSSWP
MFLLETLNGSEMASATLFKKEPPKPPLNNFKVGMKLEAIDKKNPYLICPATIGDVKGDEV
HITFDGWSGAFDYWCKYDSRDIFPAGWCRLTGDVLQPPGTS

Ligands and cofactors

ID	Name	Formula	Copies
MLZ	N-methyl-lysine	C7 H16 N2 O2	2

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

Primary citation

The Malignant Brain Tumor Repeats of Human Scml2 Bind to Peptides Containing Monomethylated Lysine. Santiveri, C.M., Lechtenberg, B.C., Allen, M.D. et al. J Mol Biol (2008) 382:1107. DOI 10.1016/J.JMB.2008.07.081 · PubMed

Other PDB entries of the same protein (UniProt Q9UQR0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2BIV 1.7 Å, Crystal structure of the wild-type MBT domains of Human SCML2
1OI1 1.78 Å, Crystal Structure of the MBT domains of Human SCML2
4EDU 2.58 Å, The MBT repeats of human SCML2 in a complex with histone H2A peptide
2MEM Solution NMR structure of SLED domain of Scml2

Browse structure collections

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