MolNFT v1 · #33490 · protein

Crystal structure of the C2B domain of RABPHILIN3A

2CM6 · Rabphilin-3A: “Crystal structure of the C2B domain of RABPHILIN3A”. X-ray diffraction, 2 ligands (CA, PO4), 2 pockets (best druggability 0.47). MolNFT v1 #33490 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2CM6
Type: protein
Length: 297 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rabphilin-3A
UniProt: P47709
Ligands: CA, PO4
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rabphilin-3A	protein	149	13% helix, 42% strand	P47709
B	Rabphilin-3A	protein	148	16% helix, 42% strand	P47709

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, B
PO4 · Phosphate ion · ion · chains B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	155	0.47	0.77	22	empty
2	161	0.46	0.76	24	empty

Interfaces

1 interface between chains.

A–B · 182 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2CM6 · crystal structure of the C2B domain of rabphilin3A · the same entry in another collection · chain A against A, TM-score 1.00
P47709 · AlphaFold monomer V2.0 prediction for rabphilin-3A (P47709) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 P47709
Elsewhere: RCSB PDB 2CM6 · PDBe 2CM6 · UniProt P47709

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