MolNFT v1 · #128663 · protein

SH3 domain from mouse cortactin (P 1 21 1 crystal form)

5NXJ · Src substrate cortactin: “SH3 domain from mouse cortactin (P 1 21 1 crystal form)”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #128663 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NXJ
Type: protein
Length: 360 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Src substrate cortactin
UniProt: Q60598
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Src substrate cortactin	protein	60	5% helix, 53% strand	Q60598

Ligands and binding sites

IPA · Isopropyl alcohol · additive · 2 copies · chains A, B, C, D

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

Pockets

5 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	665	0.69	0.77	61	empty
2	330	0.69	0.83	46	IPA
3	71	0.45	0.82	12	empty
4	54	0.38	0.80	13	empty
5	52	0.25	0.72	15	empty

Interfaces

8 interfaces between chains.

E–F · 489 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 473 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 468 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 451 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 433 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5NXJ · SH3 domain from Mouse cortactin (P 1 21 1 crystal form) · the same entry in another collection · chain C against C, TM-score 1.00
Q60598 · AlphaFold monomer V2.0 prediction for src substrate cortactin (Q60598) · 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 Q60598
Elsewhere: RCSB PDB 5NXJ · PDBe 5NXJ · UniProt Q60598

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