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Crystal structure of the wild-type mbt domains of human SCML2

Analyse Crystal structure of the wild-type mbt domains of human SCML2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BIV
Type: protein
Length: 616 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sex comb on midleg-like protein 2
UniProt: Q9UQR0
Ligands: NA, IOD
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sex comb on midleg-like protein 2	protein	212	18% helix, 29% strand	Q9UQR0
B	Sex comb on midleg-like protein 2	protein	211	15% helix, 29% strand	Q9UQR0
C	Sex comb on midleg-like protein 2	protein	193	13% helix, 32% strand	Q9UQR0

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains B, C
IOD · Iodide ion · ion · 10 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	441	0.64	0.77	64	empty
2	269	0.48	0.73	37	empty
3	134	0.44	0.76	25	empty
4	112	0.42	0.76	19	empty
5	50	0.34	0.79	12	empty

Interfaces

2 interfaces between chains.

A–B · 430 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 402 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2BIV · Crystal structure of the wild-type MBT domains of Human SCML2 · the same entry in another collection · chain B against B, TM-score 1.00
Q9UQR0 · AlphaFold monomer V2.0 prediction for sex comb on midleg-like protein 2 (Q9UQR0) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9UQR0
Elsewhere: RCSB PDB 2BIV · PDBe 2BIV · UniProt Q9UQR0

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