MolNFT v1 · #163666 · protein

Dimerization domain of xenopus laevis LDB1 in complex with darpin 10

6S9S: “Dimerization domain of xenopus laevis LDB1 in complex with darpin 10”. X-ray diffraction, 2 pockets (best druggability 0.60). MolNFT v1 #163666 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6S9S
Type: protein
Length: 325 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Darpin 10; Lim domain-binding protein 1
UniProt: P70060
Pockets: 2 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F	Darpin 10	protein	157	54% helix, 0% strand	—
A	Lim domain-binding protein 1	protein	168	29% helix, 42% strand	P70060

Pockets

2 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	266	0.60	0.79	30	empty
2	63	0.32	0.76	12	empty

Interfaces

1 interface between chains.

F–A · 1098 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6S9S · Dimerization domain of Xenopus laevis LDB1 in complex with darpin 10 · the same entry in another collection · chain F against F, TM-score 1.00
P70060 · AlphaFold monomer V2.0 prediction for lim domain-binding protein 1 (P70060) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P70060
Elsewhere: RCSB PDB 6S9S · PDBe 6S9S · UniProt P70060

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