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Crystal structure of the nco-A1 pas-B domain with yl-2

Analyse Crystal structure of the nco-A1 pas-B domain with yl-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Y7W
Type: protein
Length: 263 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor coactivator 1; Yl-2 peptide
EC: 2.3.1.48
UniProt: P70365
Ligands: NH2
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear receptor coactivator 1 (EC 2.3.1.48)	protein	125	34% helix, 31% strand	P70365
B	Nuclear receptor coactivator 1 (EC 2.3.1.48)	protein	108	26% helix, 37% strand	P70365
C, D	Yl-2 peptide	protein	15	60% helix, 0% strand	—

Ligands and binding sites

NH2 · Amino group · ion · 2 copies · chains C, D

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

Pockets

2 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	223	0.72	0.88	31	empty
2	69	0.30	0.74	13	empty

Interfaces

6 interfaces between chains.

B–D · 578 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 572 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 464 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 149 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 142 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (nonstandard).

Compared structures

5Y7W · Crystal structure of the Nco-A1 PAS-B domain with YL-2 · the same entry in another collection · chain A against A, TM-score 1.00
P70365 · AlphaFold monomer V2.0 prediction for nuclear receptor coactivator 1 (P70365) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P70365
Elsewhere: RCSB PDB 5Y7W · PDBe 5Y7W · UniProt P70365

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