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Crystal structure of the apoaequorin complex with (S)-hm-dactz

Analyse Crystal structure of the apoaequorin complex with (S)-hm-dactz in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EG3
Type: protein
Length: 3,046 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aequorin-2
UniProt: P02592
Ligands: J2U
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 7 distinct chains · 61% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aequorin-2	protein	189	61% helix, 5% strand	P02592
C, D, G, H, I, M, N	Aequorin-2	protein	190	61% helix, 6% strand	P02592
E	Aequorin-2	protein	194	59% helix, 6% strand	P02592
F	Aequorin-2	protein	191	61% helix, 5% strand	P02592
J	Aequorin-2	protein	193	62% helix, 5% strand	P02592
K, L	Aequorin-2	protein	188	62% helix, 6% strand	P02592
O, P	Aequorin-2	protein	192	61% helix, 6% strand	P02592

Ligands and binding sites

J2U · (2~{S})-6-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl) methyl]-4-(phenylmethyl)-2,3-dihydroinden-1-one · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	203	0.85	0.97	30	J2U
2	198	0.85	0.97	31	J2U
3	198	0.84	0.97	30	J2U
4	200	0.84	0.97	30	J2U
5	200	0.84	0.97	31	J2U

Interfaces

21 interfaces between chains.

E–K · 1068 Å² buried · 26 hydrogen bonds · protein-protein
C–O · 1053 Å² buried · 18 hydrogen bonds · protein-protein
D–P · 1049 Å² buried · 19 hydrogen bonds · protein-protein
G–M · 1038 Å² buried · 18 hydrogen bonds · protein-protein
C–E · 1036 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7EG3 · Crystal structure of the apoAequorin complex with (S)-HM-daCTZ · the same entry in another collection · chain K against K, 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 P02592
Elsewhere: RCSB PDB 7EG3 · PDBe 7EG3 · UniProt P02592

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