Research workbench

Crystal structure of the SAMD1 SAM domain in another crystal form

Analyse Crystal structure of the SAMD1 SAM domain in another crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LUK
Type: protein
Length: 1,380 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Atherin
UniProt: Q6SPF0
Ligands: SO4
Pockets: 16 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	Atherin	protein	69	71% helix, 0% strand	Q6SPF0

Ligands and binding sites

SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T

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

Pockets

16 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	709	0.78	0.83	69	empty
2	701	0.78	0.83	65	empty
3	228	0.65	0.84	27	empty
4	205	0.63	0.83	24	empty
5	203	0.63	0.83	25	empty

Interfaces

42 interfaces between chains.

L–O · 546 Å² buried · 10 hydrogen bonds · protein-protein
F–J · 544 Å² buried · 12 hydrogen bonds · protein-protein
K–O · 542 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 542 Å² buried · 11 hydrogen bonds · protein-protein
R–S · 532 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6LUK · Crystal structure of the SAMD1 SAM domain in another crystal form · the same entry in another collection · chain T against T, 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 Q6SPF0
Elsewhere: RCSB PDB 6LUK · PDBe 6LUK · UniProt Q6SPF0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.