MolNFT v1 · #125969 · protein

Structure of the CA2+-bound rabphilin 3A C2B domain SNAP25 complex (P21 space group)

5LOW · Rabphilin-3A: “Structure of the CA2+-bound rabphilin 3A C2B domain SNAP25 complex (P21 space group)”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.70). MolNFT v1 #125969 on GenesisL1: 3D structure, binding sites…

PDB: 5LOW
Type: protein
Length: 1,374 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rabphilin-3A; Synaptosomal-associated protein 25
UniProt: P47709, P60881
Ligands: CA
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 13 distinct chains · 44% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rabphilin-3A	protein	142	13% helix, 37% strand	P47709
B, C	Rabphilin-3A	protein	144	10% helix, 38% strand	P47709
D	Synaptosomal-associated protein 25	protein	68	93% helix, 0% strand	P60881
E	Synaptosomal-associated protein 25	protein	56	93% helix, 0% strand	P60881
F	Synaptosomal-associated protein 25	protein	68	91% helix, 0% strand	P60881
G	Synaptosomal-associated protein 25	protein	60	87% helix, 0% strand	P60881
H	Rabphilin-3A	protein	140	11% helix, 43% strand	P47709
I	Rabphilin-3A	protein	145	10% helix, 39% strand	P47709
J	Rabphilin-3A	protein	140	10% helix, 43% strand	P47709
K	Synaptosomal-associated protein 25	protein	72	89% helix, 0% strand	P60881
L	Synaptosomal-associated protein 25	protein	63	87% helix, 0% strand	P60881
M	Synaptosomal-associated protein 25	protein	72	83% helix, 0% strand	P60881
N	Synaptosomal-associated protein 25	protein	60	87% helix, 0% strand	P60881

Ligands and binding sites

CA · Calcium ion · metal · 12 copies · chains A, B, C, H, I, J
GOL · Glycerol · additive · 7 copies · chains A, B, C, H, K, M, N

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

Pockets

9 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	462	0.70	0.81	55	empty
2	372	0.64	0.79	59	empty
3	731	0.63	0.73	58	empty
4	202	0.54	0.78	24	empty
5	323	0.54	0.75	46	empty

Interfaces

32 interfaces between chains.

K–M · 1548 Å² buried · 13 hydrogen bonds · protein-protein
D–F · 1493 Å² buried · 11 hydrogen bonds · protein-protein
K–L · 1370 Å² buried · 13 hydrogen bonds · protein-protein
F–G · 1357 Å² buried · 14 hydrogen bonds · protein-protein
M–N · 1329 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5LOW · Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group) · the same entry in another collection · chain M against M, 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 P47709
Every structure of UniProt P60881
Elsewhere: RCSB PDB 5LOW · PDBe 5LOW · UniProt P47709 · UniProt P60881

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