MolNFT v1 · #7664 · protein

The crystal structure of bacteria-specific L17 ribosomal protein.

1GD8 · 50S ribosomal protein L17: “The crystal structure of bacteria-specific L17 ribosomal protein.”. X-ray diffraction, 8 pockets (best druggability 0.65). MolNFT v1 #7664 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1GD8
Type: protein
Length: 945 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L17
UniProt: Q9Z9H5
Pockets: 8 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 58% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I	50S ribosomal protein L17	protein	105	58% helix, 20% strand	Q9Z9H5

Pockets

8 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	690	0.65	0.74	51	empty
2	307	0.50	0.73	35	empty
3	127	0.41	0.76	29	empty
4	53	0.35	0.79	16	empty
5	105	0.33	0.73	22	empty

Interfaces

15 interfaces between chains.

G–H · 660 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 630 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 620 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 602 Å² buried · 8 hydrogen bonds · protein-protein
E–G · 503 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1GD8 · The crystal structure of bacteria-specific L17 ribosomal protein. · 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 Q9Z9H5
Elsewhere: RCSB PDB 1GD8 · PDBe 1GD8 · UniProt Q9Z9H5

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