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Annexin XII E105K homohexamer crystal structure

Analyse Annexin XII E105K homohexamer crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DM5
Type: protein
Length: 1,890 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Annexin XII E105K mutant homohexamer
UniProt: P26256
Ligands: CA
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Annexin XII E105K mutant homohexamer	protein	315	73% helix, 0% strand	P26256

Ligands and binding sites

CA · Calcium ion · metal · 11 copies · chains A, E, B, D, C, F

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	990	0.79	0.81	102	CA
2	975	0.78	0.81	97	CA
3	751	0.77	0.82	65	empty
4	897	0.77	0.80	97	empty
5	931	0.76	0.79	81	empty

Interfaces

12 interfaces between chains.

A–E · 1071 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 1066 Å² buried · 17 hydrogen bonds · protein-protein
C–F · 1042 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 680 Å² buried · 13 hydrogen bonds · protein-protein
D–F · 649 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

1DM5 · Annexin XII E105K homohexamer crystal structure · the same entry in another collection · chain F against F, TM-score 1.00
P26256 · AlphaFold monomer V2.0 prediction for annexin-B12 (P26256) · a predicted model of the same protein · 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 P26256
Elsewhere: RCSB PDB 1DM5 · PDBe 1DM5 · UniProt P26256

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