MolNFT v1 · #99776 · protein

CDC34-ubiquitin-CC0651 complex

4MDK · Ubiquitin-conjugating enzyme E2 R1: “CDC34-ubiquitin-CC0651 complex”. X-ray diffraction, 1 ligand (U94), 12 pockets (best druggability 0.78). MolNFT v1 #99776 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4MDK
Type: protein
Length: 953 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-conjugating enzyme E2 R1; Ubiquitin
EC: 6.3.2.19
UniProt: P49427, P0CG48
Ligands: U94
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 6 distinct chains · 32% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Ubiquitin-conjugating enzyme E2 R1 (EC 6.3.2.19)	protein	168	38% helix, 15% strand	P49427
B	Ubiquitin-conjugating enzyme E2 R1 (EC 6.3.2.19)	protein	161	37% helix, 16% strand	P49427
D	Ubiquitin-conjugating enzyme E2 R1 (EC 6.3.2.19)	protein	157	38% helix, 15% strand	P49427
E, F	Ubiquitin	protein	76	20% helix, 33% strand	P0CG48
G	Ubiquitin	protein	73	21% helix, 32% strand	P0CG48
H	Ubiquitin	protein	74	20% helix, 34% strand	P0CG48

Ligands and binding sites

U94 · 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid · ligand · 4 copies · chains A, E, B, F, C, G, D, H

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1147	0.78	0.80	104	empty
2	963	0.75	0.78	76	U94
3	361	0.68	0.81	42	U94
4	318	0.66	0.81	44	U94
5	276	0.66	0.82	36	U94

Interfaces

12 interfaces between chains.

A–E · 741 Å² buried · 13 hydrogen bonds · protein-protein
C–G · 680 Å² buried · 8 hydrogen bonds · protein-protein
B–F · 605 Å² buried · 8 hydrogen bonds · protein-protein
D–H · 595 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 405 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4MDK · Cdc34-ubiquitin-CC0651 complex · the same entry in another collection · chain H against H, TM-score 1.00
P49427 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 R1 (P49427) · a predicted model of the same protein · chain D against A, TM-score 0.96

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 P49427
Every structure of UniProt P0CG48
Elsewhere: RCSB PDB 4MDK · PDBe 4MDK · UniProt P49427 · UniProt P0CG48

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