MolNFT v1 · #175069 · protein

Drosophila melanogaster krimper ETUD2-AUBR15ME2 complex

7CFD · FI20010P1: “Drosophila melanogaster krimper ETUD2-AUBR15ME2 complex”. X-ray diffraction, 1 ligand (2MR), 20 pockets (best druggability 0.79). MolNFT v1 #175069 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7CFD
Type: protein
Length: 1,473 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FI20010P1; Protein aubergine
UniProt: A1ZAC4, O76922
Ligands: 2MR
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 13 distinct chains · 20% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D	FI20010P1	protein	178	21% helix, 39% strand	A1ZAC4
I	Protein aubergine	protein	4	0% helix, 0% strand	O76922
C	FI20010P1	protein	179	21% helix, 40% strand	A1ZAC4
J	Protein aubergine	protein	7	0% helix, 0% strand	O76922
K	Protein aubergine	protein	8	0% helix, 0% strand	O76922
E	FI20010P1	protein	180	19% helix, 36% strand	A1ZAC4
L	Protein aubergine	protein	4	0% helix, 0% strand	O76922
F	FI20010P1	protein	182	21% helix, 41% strand	A1ZAC4
A	FI20010P1	protein	176	20% helix, 42% strand	A1ZAC4
G, H	FI20010P1	protein	181	21% helix, 40% strand	A1ZAC4
N	Protein aubergine	protein	6	0% helix, 0% strand	O76922
M	Protein aubergine	protein	6	0% helix, 0% strand	O76922
Z	Protein aubergine	protein	3	0% helix, 0% strand	O76922

Ligands and binding sites

2MR · N3, N4-dimethylarginine · ligand · chains D

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	738	0.79	0.83	70	empty
2	309	0.78	0.89	46	empty
3	996	0.77	0.79	65	empty
4	341	0.76	0.87	45	empty
5	936	0.75	0.78	67	empty

Interfaces

24 interfaces between chains.

D–A · 974 Å² buried · 8 hydrogen bonds · protein-protein
E–H · 949 Å² buried · 10 hydrogen bonds · protein-protein
F–G · 947 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 940 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 806 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 modified (methylation).

Compared structures

7CFD · Drosophila melanogaster Krimper eTud2-AubR15me2 complex · the same entry in another collection · chain Z against Z, 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 A1ZAC4
Every structure of UniProt O76922
Elsewhere: RCSB PDB 7CFD · PDBe 7CFD · UniProt A1ZAC4 · UniProt O76922

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