MolNFT v1 · #54280 · protein

Crystal structure of the LMO2:LDB1-lid complex, C2 crystal form

2XJZ · Rhombotin-2: “Crystal structure of the LMO2:LDB1-lid complex, C2 crystal form”. X-ray diffraction, 2 ligands (ZN, CL), 8 pockets (best druggability 0.66). MolNFT v1 #54280 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2XJZ
Type: protein
Length: 751 residues
Chains: 10
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, CL
Pockets: 8 · best druggability 0.66

Structure

x-ray diffraction · 9 distinct chains · 16% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhombotin-2	protein	125	17% helix, 34% strand	P25791
B	Rhombotin-2	protein	122	17% helix, 34% strand	P25791
C	Rhombotin-2	protein	112	16% helix, 29% strand	P25791
D	Rhombotin-2	protein	129	16% helix, 36% strand	P25791
E	Rhombotin-2	protein	127	14% helix, 31% strand	P25791
I, L	Lim domain-binding protein 1	protein	29	10% helix, 41% strand	Q86U70
J	Lim domain-binding protein 1	protein	31	13% helix, 39% strand	Q86U70
K	Lim domain-binding protein 1	protein	21	19% helix, 29% strand	Q86U70
M	Lim domain-binding protein 1	protein	26	12% helix, 38% strand	Q86U70

Ligands and binding sites

ZN · Zinc ion · metal · 20 copies · chains A, B, C, D, E
CL · Chloride ion · ion · 2 copies · chains B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	511	0.66	0.78	53	CL
2	449	0.63	0.77	51	CL
3	333	0.58	0.76	25	empty
4	72	0.32	0.74	13	empty
5	63	0.32	0.76	15	empty

Interfaces

17 interfaces between chains.

D–L · 1833 Å² buried · 31 hydrogen bonds · protein-protein
B–J · 1798 Å² buried · 25 hydrogen bonds · protein-protein
A–I · 1795 Å² buried · 31 hydrogen bonds · protein-protein
E–M · 1668 Å² buried · 29 hydrogen bonds · protein-protein
C–K · 1217 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

2XJZ · Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form · the same entry in another collection · chain M against M, TM-score 1.00
P25791 · AlphaFold monomer V2.0 prediction for rhombotin-2 (P25791) · a predicted model of the same protein · chain D 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 P25791
Every structure of UniProt Q86U70
Elsewhere: RCSB PDB 2XJZ · PDBe 2XJZ · UniProt P25791 · UniProt Q86U70

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