MolNFT v1 · #125588 · protein

Crystal structure of the heterodimeric gef MON1-CCZ1 in complex with YPT7

5LDD: “Crystal structure of the heterodimeric gef MON1-CCZ1 in complex with YPT7”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.67). MolNFT v1 #125588 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LDD
Type: protein
Length: 955 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MON1; CCZ1; Rab small monomeric GTPase-like protein
UniProt: G0SGS3, G0SD94, G0SGE1
Ligands: SO4
Pockets: 12 · best druggability 0.67

Structure

x-ray diffraction · 6 distinct chains · 45% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MON1	protein	155	48% helix, 21% strand	G0SGS3
B	CCZ1	protein	166	46% helix, 28% strand	G0SD94
C	Rab small monomeric GTPase-like protein	protein	168	40% helix, 30% strand	G0SGE1
D	MON1	protein	143	51% helix, 22% strand	G0SGS3
E	CCZ1	protein	165	46% helix, 26% strand	G0SD94
F	Rab small monomeric GTPase-like protein	protein	158	42% helix, 30% strand	G0SGE1

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains C, F

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

Pockets

12 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	543	0.67	0.77	40	empty
2	228	0.61	0.81	37	empty
3	234	0.60	0.80	35	empty
4	246	0.55	0.77	35	empty
5	251	0.55	0.77	35	empty

Interfaces

8 interfaces between chains.

D–F · 1013 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 1011 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 999 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 996 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 644 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5LDD · Crystal structure of the heterodimeric GEF Mon1-Ccz1 in complex with Ypt7 · 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 G0SGS3
Every structure of UniProt G0SD94
Every structure of UniProt G0SGE1
Elsewhere: RCSB PDB 5LDD · PDBe 5LDD · UniProt G0SGS3 · UniProt G0SD94 · UniProt G0SGE1

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