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Crystal structure of PLEXINC1/RAP1B complex

Analyse Crystal structure of PLEXINC1/RAP1B complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4M8N
Type: protein
Length: 2,934 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PLEXINC1 intracellular region; RAS-related protein rap-1B
UniProt: Q5RGW1, P61224
Ligands: GDP, AF3, MG
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 7 distinct chains · 51% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	PLEXINC1 intracellular region	protein	574	56% helix, 7% strand	Q5RGW1
B	PLEXINC1 intracellular region	protein	571	57% helix, 7% strand	Q5RGW1
C	PLEXINC1 intracellular region	protein	560	54% helix, 8% strand	Q5RGW1
D	PLEXINC1 intracellular region	protein	560	54% helix, 7% strand	Q5RGW1
E, G	RAS-related protein rap-1B	protein	168	34% helix, 25% strand	P61224
F	RAS-related protein rap-1B	protein	166	35% helix, 25% strand	P61224
H	RAS-related protein rap-1B	protein	167	31% helix, 25% strand	P61224

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, E, C, F, B, G, D, H
AF3 · Aluminum fluoride · ligand · 4 copies · chains A, E, C, F, B, G, D, H
MG · Magnesium ion · metal · 4 copies · chains E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	907	0.77	0.80	97	empty
2	527	0.77	0.84	68	MG, GDP, AF3
3	527	0.77	0.84	67	GDP, AF3
4	519	0.76	0.84	69	MG, GDP, AF3
5	520	0.76	0.84	71	MG, GDP, AF3

Interfaces

12 interfaces between chains.

D–H · 1870 Å² buried · 19 hydrogen bonds · protein-protein
C–F · 1810 Å² buried · 24 hydrogen bonds · protein-protein
B–G · 1766 Å² buried · 20 hydrogen bonds · protein-protein
A–E · 1756 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 1556 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4M8N · Crystal Structure of PlexinC1/Rap1B Complex · the same entry in another collection · chain H against H, TM-score 1.00
P61224 · AlphaFold monomer V2.0 prediction for RAS-related protein rap-1B (P61224) · a predicted model of the same protein · chain F against A, TM-score 0.98

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 Q5RGW1
Every structure of UniProt P61224
Elsewhere: RCSB PDB 4M8N · PDBe 4M8N · UniProt Q5RGW1 · UniProt P61224

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