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Crystal structure of E. histolytica racc bound to the EHPAK4 pbd

Analyse Crystal structure of E. histolytica racc bound to the EHPAK4 pbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MIT
Type: protein
Length: 879 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rho family GTPase; SERINE/THREONINE protein kinase pak, putative
EC: 3.6.5.2
UniProt: M7WE85, N9UZ59
Ligands: GTP, MG
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 7 distinct chains · 36% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rho family GTPase (EC 3.6.5.2)	protein	178	39% helix, 26% strand	M7WE85
B	Rho family GTPase (EC 3.6.5.2)	protein	179	40% helix, 25% strand	M7WE85
C, D	Rho family GTPase (EC 3.6.5.2)	protein	181	39% helix, 25% strand	M7WE85
E	SERINE/THREONINE protein kinase pak, putative	protein	40	23% helix, 45% strand	N9UZ59
F	SERINE/THREONINE protein kinase pak, putative	protein	35	26% helix, 40% strand	N9UZ59
G	SERINE/THREONINE protein kinase pak, putative	protein	43	21% helix, 42% strand	N9UZ59
H	SERINE/THREONINE protein kinase pak, putative	protein	42	21% helix, 43% strand	N9UZ59

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 12 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	396	0.75	0.85	54	GTP, MG
2	420	0.74	0.84	55	GTP, MG
3	249	0.58	0.79	44	GTP, MG
4	232	0.57	0.79	39	GTP, MG
5	131	0.56	0.83	21	empty

Interfaces

12 interfaces between chains.

C–G · 1315 Å² buried · 19 hydrogen bonds · protein-protein
D–H · 1273 Å² buried · 17 hydrogen bonds · protein-protein
A–E · 1212 Å² buried · 25 hydrogen bonds · protein-protein
B–F · 1113 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 455 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4MIT · Crystal structure of E. histolytica RacC bound to the EhPAK4 PBD · the same entry in another collection · chain A against A, 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 M7WE85
Every structure of UniProt N9UZ59
Elsewhere: RCSB PDB 4MIT · PDBe 4MIT · UniProt M7WE85 · UniProt N9UZ59

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