MolNFT v1 · #139740 · protein

Crystal structure of N-terminal domain EHCABP1 ef-2 mutant

5XOP · Calcium-binding protein 1 (EHCBP1), putative: “Crystal structure of N-terminal domain EHCABP1 ef-2 mutant”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.75). MolNFT v1 #139740 on GenesisL1: 3D structure, binding…

PDB: 5XOP
Type: protein
Length: 395 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calcium-binding protein 1 (EHCBP1), putative
UniProt: M3TKH6
Ligands: CA
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 69% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Calcium-binding protein 1 (EHCBP1), putative	protein	66	68% helix, 8% strand	M3TKH6
F	Calcium-binding protein 1 (EHCBP1), putative	protein	65	69% helix, 8% strand	M3TKH6

Ligands and binding sites

CA · Calcium ion · metal · 13 copies · chains A, B, C, D, E, F
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains D, E

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

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	875	0.75	0.78	67	empty
2	316	0.63	0.79	31	empty
3	314	0.61	0.78	34	empty
4	270	0.59	0.78	25	empty
5	269	0.58	0.77	29	empty

Interfaces

9 interfaces between chains.

D–E · 639 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 595 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 594 Å² buried · 5 hydrogen bonds · protein-protein
E–F · 591 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 584 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5XOP · Crystal Structure of N-terminal domain EhCaBP1 EF-2 mutant · the same entry in another collection · chain A against A, 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 M3TKH6
Elsewhere: RCSB PDB 5XOP · PDBe 5XOP · UniProt M3TKH6

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