MolNFT v1 · #175416 · protein

Crystal structure of SLX1-SLX4

7CQ2 · Structure-specific endonuclease subunit SLX1: “Crystal structure of SLX1-SLX4”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.56). MolNFT v1 #175416 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7CQ2
Type: protein
Length: 716 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Structure-specific endonuclease subunit SLX1; SLX4 isoform 1
EC: 3.1.-.-
UniProt: A6ZLG6, A0A6A5PU22
Ligands: ZN
Pockets: 10 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Structure-specific endonuclease subunit SLX1 (EC 3.1.-.-)	protein	274	45% helix, 18% strand	A6ZLG6
B	Structure-specific endonuclease subunit SLX1 (EC 3.1.-.-)	protein	297	37% helix, 18% strand	A6ZLG6
C	SLX4 isoform 1	protein	74	64% helix, 5% strand	A0A6A5PU22
D	SLX4 isoform 1	protein	71	65% helix, 6% strand	A0A6A5PU22

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

10 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	264	0.56	0.77	44	empty
2	180	0.51	0.78	31	empty
3	132	0.49	0.79	20	empty
4	120	0.48	0.79	21	empty
5	148	0.44	0.75	23	empty

Interfaces

3 interfaces between chains.

A–C · 1347 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 1174 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1031 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7CQ2 · Crystal structure of Slx1-Slx4 · the same entry in another collection · chain A against A, TM-score 1.00
A6ZLG6 · AlphaFold monomer V2.0 prediction for structure-specific endonuclease subunit SLX1… · a predicted model of the same protein · chain B against A, TM-score 0.95

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 A6ZLG6
Every structure of UniProt A0A6A5PU22
Elsewhere: RCSB PDB 7CQ2 · PDBe 7CQ2 · UniProt A6ZLG6 · UniProt A0A6A5PU22

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