MolNFT v1 · #145469 · protein

Sidc in complex with UBCH7~UB

6CP2: “Sidc in complex with UBCH7~UB”. X-ray diffraction, 6 pockets (best druggability 0.86). MolNFT v1 #145469 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6CP2
Type: protein
Length: 733 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sidc; Ubiquitin-conjugating enzyme E2 L3; Polyubiquitin-B
EC: 2.3.2.23
UniProt: Q6RCR4, P68036, P0CG47
Pockets: 6 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sidc	protein	502	44% helix, 10% strand	Q6RCR4
B	Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23)	protein	153	35% helix, 18% strand	P68036
C	Polyubiquitin-B	protein	78	19% helix, 37% strand	P0CG47

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1050	0.86	0.87	127	empty
2	301	0.73	0.86	50	empty
3	74	0.53	0.86	16	empty
4	51	0.51	0.88	15	empty
5	131	0.44	0.77	23	empty

Interfaces

3 interfaces between chains.

A–C · 1321 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1278 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 98 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

6CP2 · SidC in complex with UbcH7~Ub · the same entry in another collection · chain A against A, TM-score 1.00
P68036 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 L3 (P68036) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q6RCR4
Every structure of UniProt P68036
Every structure of UniProt P0CG47
Elsewhere: RCSB PDB 6CP2 · PDBe 6CP2 · UniProt Q6RCR4 · UniProt P68036 · UniProt P0CG47

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