MolNFT v1 · #181272 · protein

Crystal structure of DDB1-crbn-ALV1 complex bound to helios (IKZF2 ZF2)

7LPS · DNA damage-binding protein 1: “Crystal structure of DDB1-crbn-ALV1 complex bound to helios (IKZF2 ZF2)”. X-ray diffraction, 2 ligands (RN9, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #181272 on GenesisL1: 3D structure…

PDB: 7LPS
Type: protein
Length: 4,758 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA damage-binding protein 1; Protein cereblon; Zinc finger protein helios
UniProt: Q16531, Q96SW2, Q9UKS7
Ligands: RN9, ZN
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	DNA damage-binding protein 1	protein	781	7% helix, 51% strand	Q16531
B, E, H, K	Protein cereblon	protein	381	27% helix, 32% strand	Q96SW2
C, I	Zinc finger protein helios	protein	29	41% helix, 14% strand	Q9UKS7
F, L	Zinc finger protein helios	protein	28	43% helix, 14% strand	Q9UKS7
G, J	DNA damage-binding protein 1	protein	779	7% helix, 51% strand	Q16531

Ligands and binding sites

RN9 · 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide · ligand · 4 copies · chains B, C, E, F, H, I, K, L
ZN · Zinc ion · metal · 8 copies · chains B, C, E, F, H, I, K, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1065	0.87	0.88	85	empty
2	1045	0.87	0.88	88	empty
3	1148	0.87	0.88	101	empty
4	1062	0.87	0.88	85	empty
5	1005	0.82	0.83	94	empty

Interfaces

17 interfaces between chains.

D–E · 2620 Å² buried · 20 hydrogen bonds · protein-protein
J–K · 2615 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2609 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2562 Å² buried · 20 hydrogen bonds · protein-protein
A–E · 564 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7LPS · Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) · the same entry in another collection · chain L against L, 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 Q16531
Every structure of UniProt Q96SW2
Every structure of UniProt Q9UKS7
Elsewhere: RCSB PDB 7LPS · PDBe 7LPS · UniProt Q16531 · UniProt Q96SW2 · UniProt Q9UKS7

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