MolNFT v1 · #58720 · protein

Crystal structure of the complex RAB27A-SLP2A

3BC1 · RAS-related protein rab-27A: “Crystal structure of the complex RAB27A-SLP2A”. X-ray diffraction, 2 ligands (GNP, MG), 6 pockets (best druggability 0.82). MolNFT v1 #58720 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3BC1
Type: protein
Length: 463 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-27A; Synaptotagmin-like protein 2
EC: 3.6.5.2
UniProt: Q9ERI2, Q9HCH5
Ligands: GNP, MG
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-27A (EC 3.6.5.2)	protein	185	36% helix, 24% strand	Q9ERI2
B	Synaptotagmin-like protein 2	protein	52	85% helix, 0% strand	Q9HCH5
E	RAS-related protein rab-27A (EC 3.6.5.2)	protein	175	40% helix, 26% strand	Q9ERI2
F	Synaptotagmin-like protein 2	protein	51	76% helix, 0% strand	Q9HCH5

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, E
MG · Magnesium ion · metal · 2 copies · chains A, E

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

Pockets

6 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	992	0.82	0.83	75	empty
2	237	0.64	0.82	30	empty
3	195	0.58	0.81	34	GNP, MG
4	219	0.58	0.79	39	GNP, MG
5	62	0.30	0.74	12	empty

Interfaces

6 interfaces between chains.

A–B · 1051 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1039 Å² buried · 9 hydrogen bonds · protein-protein
B–E · 555 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 483 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 224 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3BC1 · Crystal Structure of the complex Rab27a-Slp2a · the same entry in another collection · chain F against F, TM-score 1.00
Q9ERI2 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-27A (Q9ERI2) · a predicted model of the same protein · chain E against A, TM-score 0.99
Q9HCH5 · AlphaFold monomer V2.0 prediction for synaptotagmin-like protein 2 (Q9HCH5) · a predicted model of the same protein · chain F against A, TM-score 0.89

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 Q9ERI2
Every structure of UniProt Q9HCH5
Elsewhere: RCSB PDB 3BC1 · PDBe 3BC1 · UniProt Q9ERI2 · UniProt Q9HCH5

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