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Structure of RASGRP2 in complex with RAP1B

Analyse Structure of RASGRP2 in complex with RAP1B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AXF
Type: protein
Length: 4,347 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS guanyl-releasing protein 2; RAS-related protein rap-1B
UniProt: Q7LDG7, P61224
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 65% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS guanyl-releasing protein 2	protein	380	68% helix, 3% strand	Q7LDG7
B, D, H, J, L, N, P	RAS-related protein rap-1B	protein	167	40% helix, 26% strand	P61224
C, E, G	RAS guanyl-releasing protein 2	protein	381	68% helix, 3% strand	Q7LDG7
F	RAS-related protein rap-1B	protein	166	36% helix, 26% strand	P61224
I	RAS guanyl-releasing protein 2	protein	372	69% helix, 2% strand	Q7LDG7
K	RAS guanyl-releasing protein 2	protein	372	71% helix, 2% strand	Q7LDG7
M	RAS guanyl-releasing protein 2	protein	375	69% helix, 2% strand	Q7LDG7
O	RAS guanyl-releasing protein 2	protein	370	69% helix, 2% strand	Q7LDG7

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	1147	0.83	0.84	102	empty
2	677	0.80	0.84	89	empty
3	683	0.73	0.79	92	empty
4	726	0.72	0.78	82	empty
5	635	0.70	0.78	64	empty

Interfaces

25 interfaces between chains.

C–D · 1657 Å² buried · 23 hydrogen bonds · protein-protein
K–L · 1642 Å² buried · 22 hydrogen bonds · protein-protein
M–N · 1633 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 1630 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 1624 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 72 modified (engineered).

Compared structures

6AXF · Structure of RasGRP2 in complex with Rap1B · the same entry in another collection · chain P against P, 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 Q7LDG7
Every structure of UniProt P61224
Elsewhere: RCSB PDB 6AXF · PDBe 6AXF · UniProt Q7LDG7 · UniProt P61224

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