MolNFT v1 · #54279 · protein

Crystal structure of the LMO2:LDB1-lid complex, P21 crystal form

2XJY · Rhombotin-2: “Crystal structure of the LMO2:LDB1-lid complex, P21 crystal form”. X-ray diffraction, 1 ligand (ZN). MolNFT v1 #54279 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XJY
Type: protein
Length: 166 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhombotin-2; Lim domain-binding protein 1
UniProt: P25791, Q86U70
Ligands: ZN

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhombotin-2	protein	131	17% helix, 34% strand	P25791
B	Lim domain-binding protein 1	protein	35	0% helix, 29% strand	Q86U70

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A

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

Interfaces

1 interface between chains.

A–B · 1810 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

2XJY · Crystal structure of the LMO2:LDB1-LID complex, P21 crystal form · the same entry in another collection · chain A against A, TM-score 1.00
P25791 · AlphaFold monomer V2.0 prediction for rhombotin-2 (P25791) · a predicted model of the same protein · chain A against A, TM-score 0.83
Q86U70 · AlphaFold monomer V2.0 prediction for lim domain-binding protein 1 (Q86U70) · a predicted model of the same protein · chain B against A, TM-score 0.30

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 P25791
Every structure of UniProt Q86U70
Elsewhere: RCSB PDB 2XJY · PDBe 2XJY · UniProt P25791 · UniProt Q86U70

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