MolNFT v1 · #90244 · protein

Crystal structure of beta-parvin CH2 domain in complex with paxillin LD1 motif

4EDN: “Crystal structure of beta-parvin CH2 domain in complex with paxillin LD1 motif”. X-ray diffraction, 2 ligands (ACE, SO4), 19 pockets (best druggability 0.75). MolNFT v1 #90244 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4EDN
Type: protein
Length: 1,346 residues
Chains: 17
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-parvin; Paxillin
UniProt: Q9HBI1, P49023
Ligands: ACE, SO4
Pockets: 19 · best druggability 0.75

Structure

x-ray diffraction · 10 distinct chains · 61% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Beta-parvin	protein	127	63% helix, 0% strand	Q9HBI1
B	Beta-parvin	protein	126	63% helix, 0% strand	Q9HBI1
D, F, G, H, J	Beta-parvin	protein	125	57% helix, 0% strand	Q9HBI1
I	Beta-parvin	protein	124	63% helix, 0% strand	Q9HBI1
K, N	Paxillin	protein	12	75% helix, 0% strand	P49023
L	Paxillin	protein	19	16% helix, 0% strand	P49023
M	Paxillin	protein	10	70% helix, 0% strand	P49023
O	Paxillin	protein	12	75% helix, 0% strand	P49023
P	Paxillin	protein	11	82% helix, 0% strand	P49023
Q	Paxillin	protein	14	64% helix, 0% strand	P49023

Ligands and binding sites

ACE · Acetyl group · ligand · chains D, L
SO4 · Sulfate ion · ion · chains C

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

Pockets

19 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	811	0.75	0.79	67	empty
2	456	0.61	0.76	36	empty
3	172	0.58	0.81	29	empty
4	249	0.53	0.76	38	empty
5	105	0.49	0.81	26	empty

Interfaces

24 interfaces between chains.

F–I · 772 Å² buried · 8 hydrogen bonds · protein-protein
C–G · 768 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 741 Å² buried · 6 hydrogen bonds · protein-protein
E–H · 733 Å² buried · 6 hydrogen bonds · protein-protein
B–J · 731 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

4EDN · Crystal structure of beta-parvin CH2 domain in complex with paxillin LD1 motif · the same entry in another collection · chain Q against Q, TM-score 1.00

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 Q9HBI1
Every structure of UniProt P49023
Elsewhere: RCSB PDB 4EDN · PDBe 4EDN · UniProt Q9HBI1 · UniProt P49023

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.