MolNFT v1 · #144778 · protein

Crystal structure of B-myb-LIN9-LIN52 complex

6C48 · Protein lin-9 homolog: “Crystal structure of B-myb-LIN9-LIN52 complex”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.59). MolNFT v1 #144778 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6C48
Type: protein
Length: 335 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein lin-9 homolog; Myb-related protein B; Protein lin-52 homolog
UniProt: Q5TKA1, P10244, Q52LA3
Ligands: SO4
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 4 distinct chains · 78% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein lin-9 homolog	protein	84	80% helix, 5% strand	Q5TKA1
D	Protein lin-9 homolog	protein	87	82% helix, 5% strand	Q5TKA1
F, C	Myb-related protein B	protein	28	68% helix, 0% strand	P10244
B, E	Protein lin-52 homolog	protein	54	74% helix, 0% strand	Q52LA3

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, F, B, E, D, C

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

Pockets

4 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	163	0.59	0.83	26	empty
2	130	0.40	0.74	13	empty
3	73	0.30	0.73	12	empty
4	50	0.27	0.74	11	empty

Interfaces

13 interfaces between chains.

A–B · 1542 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 1541 Å² buried · 10 hydrogen bonds · protein-protein
F–E · 746 Å² buried · 3 hydrogen bonds · protein-protein
C–B · 725 Å² buried · 4 hydrogen bonds · protein-protein
D–F · 605 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (engineered).

Compared structures

6C48 · Crystal structure of B-Myb-LIN9-LIN52 complex · the same entry in another collection · chain E against E, TM-score 1.00
Q5TKA1 · AlphaFold monomer V2.0 prediction for protein lin-9 homolog (Q5TKA1) · a predicted model of the same protein · chain D against A, TM-score 0.97
Q52LA3 · AlphaFold monomer V2.0 prediction for protein lin-52 homolog (Q52LA3) · a predicted model of the same protein · chain B against A, TM-score 0.75
P10244 · AlphaFold monomer V2.0 prediction for myb-related protein B (P10244) · a predicted model of the same protein · chain F against A, TM-score 0.64

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 Q5TKA1
Every structure of UniProt P10244
Every structure of UniProt Q52LA3
Elsewhere: RCSB PDB 6C48 · PDBe 6C48 · UniProt Q5TKA1 · UniProt P10244 · UniProt Q52LA3

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