MolNFT v1 · #166683 · protein

Crystal structure of bak core domain BH3-groove-dimer in complex with ddm

6UXO · BCL-2 homologous ANTAGONIST/KILLER: “Crystal structure of bak core domain BH3-groove-dimer in complex with ddm”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.84). MolNFT v1 #166683 on GenesisL1: 3D structure…

PDB: 6UXO
Type: protein
Length: 955 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2 homologous ANTAGONIST/KILLER
UniProt: Q16611
Ligands: SO4
Pockets: 8 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 81% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	BCL-2 homologous ANTAGONIST/KILLER	protein	80	83% helix, 0% strand	Q16611
B, H, J	BCL-2 homologous ANTAGONIST/KILLER	protein	78	82% helix, 0% strand	Q16611
C, G, I	BCL-2 homologous ANTAGONIST/KILLER	protein	81	79% helix, 0% strand	Q16611
D, F, K	BCL-2 homologous ANTAGONIST/KILLER	protein	79	81% helix, 0% strand	Q16611
L	BCL-2 homologous ANTAGONIST/KILLER	protein	81	79% helix, 0% strand	Q16611

Ligands and binding sites

SO4 · Sulfate ion · ion · 35 copies · chains A, B, F, C, D, E, G, L, J, H, I, K
EDO · 1,2-ethanediol · additive · 25 copies · chains A, B, D, L, E, C, F, G, H, I, J, K
LMT · Dodecyl-beta-D-maltoside · additive · 24 copies · chains A, B, C, D, E, F, G, H, K, I, J, L
ACT · Acetate ion · additive · 6 copies · chains A, B, E, F, C, D, G, K, L, H, I, J

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

Pockets

8 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	1062	0.84	0.85	103	SO4, ACT, EDO
2	888	0.81	0.84	87	SO4, ACT, EDO
3	101	0.55	0.85	22	empty
4	67	0.51	0.86	19	empty
5	76	0.50	0.85	21	empty

Interfaces

38 interfaces between chains.

K–L · 1958 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1957 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1953 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1944 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1935 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

6UXO · Crystal structure of BAK core domain BH3-groove-dimer in complex with DDM · the same entry in another collection · chain L against L, 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 Q16611
Elsewhere: RCSB PDB 6UXO · PDBe 6UXO · UniProt Q16611

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