MolNFT v1 · #89385 · protein

Crystal structure of DAD2 S96A mutant

4DNQ: “Crystal structure of DAD2 S96A mutant”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #89385 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4DNQ
Type: protein
Length: 3,153 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DAD2
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, H, K	DAD2	protein	262	47% helix, 18% strand	—
C, D, F, G, J	DAD2	protein	263	47% helix, 18% strand	—
I, L	DAD2	protein	264	47% helix, 18% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1085	0.85	0.86	113	empty
2	1168	0.82	0.83	105	empty
3	895	0.82	0.84	92	empty
4	906	0.81	0.83	85	empty
5	1119	0.80	0.81	104	empty

Interfaces

21 interfaces between chains.

C–E · 715 Å² buried · 16 hydrogen bonds · protein-protein
C–G · 698 Å² buried · 14 hydrogen bonds · protein-protein
E–H · 622 Å² buried · 3 hydrogen bonds · protein-protein
G–K · 603 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 598 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4DNQ · Crystal Structure of DAD2 S96A 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
Elsewhere: RCSB PDB 4DNQ · PDBe 4DNQ

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