Research workbench

Crystal structure of HDLG1-PDZ2 complexed with apc

Analyse Crystal structure of HDLG1-PDZ2 complexed with apc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RL8
Type: protein
Length: 469 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Disks large homolog 1; 11-mer peptide from adenomatous polyposis COLI protein
UniProt: Q12959, P25054
Pockets: 10 · best druggability 0.54

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Disks large homolog 1	protein	94	15% helix, 40% strand	Q12959
B, E	Disks large homolog 1	protein	90	16% helix, 42% strand	Q12959
C	Disks large homolog 1	protein	95	15% helix, 38% strand	Q12959
F	11-mer peptide from adenomatous polyposis COLI protein	protein	6	0% helix, 17% strand	P25054

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	258	0.54	0.76	32	empty
2	79	0.51	0.84	20	empty
3	134	0.50	0.79	25	empty
4	168	0.47	0.76	27	empty
5	75	0.36	0.76	12	empty

Interfaces

7 interfaces between chains.

C–D · 663 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 606 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 367 Å² buried · 3 hydrogen bonds · protein-protein
B–F · 322 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 242 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3RL8 · Crystal structure of hDLG1-PDZ2 complexed with APC · the same entry in another collection · chain F against F, TM-score 1.00
Q12959 · AlphaFold monomer V2.0 prediction for disks large homolog 1 (Q12959) · a predicted model of the same protein · chain E 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 Q12959
Every structure of UniProt P25054
Elsewhere: RCSB PDB 3RL8 · PDBe 3RL8 · UniProt Q12959 · UniProt P25054

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