MolNFT v1 · #140511 · protein

Crystal structure of schlafen 13 (SLFN13) N'-domain

5YD0 · Schlafen 8: “Crystal structure of schlafen 13 (SLFN13) N'-domain”. X-ray diffraction, 1 ligand (ZN), 15 pockets (best druggability 0.53). MolNFT v1 #140511 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YD0
Type: protein
Length: 1,300 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Schlafen 8
UniProt: Q5U311
Ligands: ZN
Pockets: 15 · best druggability 0.53

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Schlafen 8	protein	327	31% helix, 24% strand	Q5U311
B	Schlafen 8	protein	331	30% helix, 24% strand	Q5U311
C	Schlafen 8	protein	316	28% helix, 21% strand	Q5U311
D	Schlafen 8	protein	326	29% helix, 24% strand	Q5U311

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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

Pockets

15 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	157	0.53	0.80	33	empty
2	183	0.50	0.77	36	empty
3	60	0.44	0.83	16	empty
4	75	0.44	0.81	20	empty
5	127	0.43	0.76	18	empty

Interfaces

4 interfaces between chains.

C–D · 891 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 839 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 814 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 792 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5YD0 · Crystal structure of Schlafen 13 (SLFN13) N'-domain · the same entry in another collection · chain D against D, TM-score 1.00
Q5U311 · AlphaFold monomer V2.0 prediction for schlafen family member 13 (Q5U311) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q5U311
Elsewhere: RCSB PDB 5YD0 · PDBe 5YD0 · UniProt Q5U311

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