MolNFT v1 · #31527 · protein + DNA

Crystal structure of KH1 domain of human POLY(C)-binding protein-2 with C-rich strand of human telomeric DNA

2AXY: “Crystal structure of KH1 domain of human POLY(C)-binding protein-2 with C-rich strand of human telomeric DNA”. X-ray diffraction, 1 pocket (best druggability 0.69). MolNFT v1 #31527 on GenesisL1: 3D structure, binding sites and…

PDB: 2AXY
Type: protein + DNA
Length: 309 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-rich strand of human telomeric DNA; POLY(RC)-binding protein 2
UniProt: Q15366
Pockets: 1 · best druggability 0.69

Structure

x-ray diffraction · 6 distinct chains · 51% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	C-rich strand of human telomeric DNA	dna	7	—	—
F	C-rich strand of human telomeric DNA	dna	5	—	—
G	C-rich strand of human telomeric DNA	dna	6	—	—
H	C-rich strand of human telomeric DNA	dna	5	—	—
A, C	POLY(RC)-binding protein 2	protein	72	51% helix, 28% strand	Q15366
B, D	POLY(RC)-binding protein 2	protein	71	51% helix, 31% strand	Q15366

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	701	0.69	0.77	72	empty

Interfaces

10 interfaces between chains.

A–B · 1008 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 962 Å² buried · 14 hydrogen bonds · protein-protein
G–C · 578 Å² buried · 14 hydrogen bonds · protein-nucleic
H–D · 548 Å² buried · 16 hydrogen bonds · protein-nucleic
F–B · 548 Å² buried · 14 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

2AXY · Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of… · the same entry in another collection · chain D against D, TM-score 1.00
Q15366 · AlphaFold monomer V2.0 prediction for POLY(RC)-binding protein 2 (Q15366) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 Q15366
Elsewhere: RCSB PDB 2AXY · PDBe 2AXY · UniProt Q15366

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