MolNFT v1 · #33967 · protein

Crystal structure of the radixin ferm domain complexed with the nherf-1 C-terminal tail peptide

2D10: “Crystal structure of the radixin ferm domain complexed with the nherf-1 C-terminal tail peptide”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #33967 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2D10
Type: protein
Length: 1,266 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Radixin; Ezrin-radixin-moesin binding phosphoprotein 50
UniProt: P26043, O14745
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Radixin	protein	295	37% helix, 25% strand	P26043
B, C, D	Radixin	protein	297	37% helix, 25% strand	P26043
E, F, G, H	Ezrin-radixin-moesin binding phosphoprotein 50	protein	20	40% helix, 0% strand	O14745

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1014	0.78	0.80	80	empty
2	982	0.78	0.80	83	empty
3	557	0.68	0.78	50	empty
4	377	0.64	0.78	29	empty
5	232	0.63	0.82	32	empty

Interfaces

10 interfaces between chains.

B–C · 1343 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1242 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 870 Å² buried · 4 hydrogen bonds · protein-protein
D–H · 859 Å² buried · 13 hydrogen bonds · protein-protein
C–G · 856 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

2D10 · Crystal structure of the Radixin FERM domain complexed with the NHERF-1 C-terminal tail… · the same entry in another collection · chain H against H, TM-score 1.00
P26043 · AlphaFold monomer V2.0 prediction for radixin (P26043) · a predicted model of the same protein · chain B against A, TM-score 0.98
O14745 · AlphaFold monomer V2.0 prediction for NA(+)/H(+) exchange regulatory cofactor nhe-RF1… · a predicted model of the same protein · chain E against A, TM-score 0.52

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 P26043
Every structure of UniProt O14745
Elsewhere: RCSB PDB 2D10 · PDBe 2D10 · UniProt P26043 · UniProt O14745

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