MolNFT v1 · #33021 · protein

Human rabex-5 residues 1-74 in complex with ubiquitin

2C7N · Rab guanine nucleotide exchange factor 1: “Human rabex-5 residues 1-74 in complex with ubiquitin”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.77). MolNFT v1 #33021 on GenesisL1: 3D structure, binding sites and…

PDB: 2C7N
Type: protein
Length: 754 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rab guanine nucleotide exchange factor 1; Ubiquitin
UniProt: Q53FG0, P62990
Ligands: ZN
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 8 distinct chains · 49% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rab guanine nucleotide exchange factor 1	protein	55	69% helix, 0% strand	Q53FG0
B, D, F, L	Ubiquitin	protein	73	25% helix, 36% strand	P62990
C	Rab guanine nucleotide exchange factor 1	protein	56	66% helix, 4% strand	Q53FG0
E, K	Rab guanine nucleotide exchange factor 1	protein	48	65% helix, 8% strand	Q53FG0
G	Rab guanine nucleotide exchange factor 1	protein	54	69% helix, 7% strand	Q53FG0
H	Ubiquitin	protein	72	24% helix, 35% strand	P62990
I	Rab guanine nucleotide exchange factor 1	protein	58	71% helix, 7% strand	Q53FG0
J	Ubiquitin	protein	71	27% helix, 32% strand	P62990

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, C, E, G, I, K

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

Pockets

12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	524	0.77	0.84	51	empty
2	238	0.51	0.75	33	empty
3	143	0.47	0.77	20	empty
4	152	0.46	0.76	22	empty
5	174	0.43	0.74	20	empty

Interfaces

17 interfaces between chains.

A–B · 787 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 774 Å² buried · 7 hydrogen bonds · protein-protein
I–J · 667 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 653 Å² buried · 12 hydrogen bonds · protein-protein
K–L · 617 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

2C7N · Human Rabex-5 residues 1-74 in complex with Ubiquitin · 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 Q53FG0
Every structure of UniProt P62990
Elsewhere: RCSB PDB 2C7N · PDBe 2C7N · UniProt Q53FG0 · UniProt P62990

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