MolNFT v1 · #143711 · protein

Crystal structure of legionella effector sded (LPG2509) in complex with ubiquitin

6B7M: “Crystal structure of legionella effector sded (LPG2509) in complex with ubiquitin”. X-ray diffraction, 3 pockets (best druggability 0.67). MolNFT v1 #143711 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6B7M
Type: protein
Length: 464 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sded (LPG2509); Polyubiquitin-C
UniProt: Q5ZSK8, P0CG48
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sded (LPG2509)	protein	312	56% helix, 4% strand	Q5ZSK8
B, C	Polyubiquitin-C	protein	76	24% helix, 32% strand	P0CG48

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	537	0.67	0.77	57	empty
2	74	0.43	0.81	15	empty
3	87	0.38	0.77	16	empty

Interfaces

2 interfaces between chains.

A–B · 1459 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 801 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6B7M · Crystal structure of Legionella effector sdeD (lpg2509) in complex with Ubiquitin · the same entry in another collection · chain B against B, 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 Q5ZSK8
Every structure of UniProt P0CG48
Elsewhere: RCSB PDB 6B7M · PDBe 6B7M · UniProt Q5ZSK8 · UniProt P0CG48

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