Research workbench

Human ncam, FN3 domains 1 and 2, M610R mutant

Analyse Human ncam, FN3 domains 1 and 2, M610R mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VKX
Type: protein
Length: 1,191 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neural cell adhesion molecule
UniProt: P13591
Ligands: SO4
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, F	Neural cell adhesion molecule	protein	198	3% helix, 49% strand	P13591
B	Neural cell adhesion molecule	protein	197	4% helix, 49% strand	P13591
E	Neural cell adhesion molecule	protein	202	3% helix, 48% strand	P13591

Ligands and binding sites

SO4 · Sulfate ion · ion · 11 copies · chains A, C, E, D, F

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	97	0.77	0.98	25	empty
2	95	0.76	0.97	26	empty
3	93	0.76	0.97	27	empty
4	75	0.74	0.98	16	empty
5	296	0.58	0.77	32	empty

Interfaces

12 interfaces between chains.

A–B · 1835 Å² buried · 39 hydrogen bonds · protein-protein
E–F · 1784 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 1736 Å² buried · 34 hydrogen bonds · protein-protein
B–E · 765 Å² buried · 11 hydrogen bonds · protein-protein
C–F · 727 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

2VKX · Human NCAM, FN3 domains 1 and 2, M610R mutant · the same entry in another collection · chain F against F, TM-score 1.00
P13591 · AlphaFold monomer V2.0 prediction for neural cell adhesion molecule 1 (P13591) · a predicted model of the same protein · chain B against A, TM-score 0.66

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 P13591
Elsewhere: RCSB PDB 2VKX · PDBe 2VKX · UniProt P13591

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