MolNFT v1 · #159078 · protein

BH3 domain swapped dimer of a bak fragment

6ODH · BCL-2 homologous ANTAGONIST/KILLER: “BH3 domain swapped dimer of a bak fragment”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.68). MolNFT v1 #159078 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ODH
Type: protein
Length: 452 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2 homologous ANTAGONIST/KILLER
UniProt: Q16611
Ligands: SO4
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 4 distinct chains · 83% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2 homologous ANTAGONIST/KILLER	protein	76	83% helix, 0% strand	Q16611
B, F	BCL-2 homologous ANTAGONIST/KILLER	protein	74	85% helix, 0% strand	Q16611
C	BCL-2 homologous ANTAGONIST/KILLER	protein	78	82% helix, 0% strand	Q16611
D, E	BCL-2 homologous ANTAGONIST/KILLER	protein	75	83% helix, 0% strand	Q16611

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C, E, F, D
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D, F

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	685	0.68	0.76	56	PEG, EPE
2	705	0.68	0.75	51	EPE, SO4
3	676	0.67	0.75	52	EPE

Interfaces

12 interfaces between chains.

A–B · 1785 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1756 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1712 Å² buried · 16 hydrogen bonds · protein-protein
D–F · 331 Å² buried · 4 hydrogen bonds · protein-protein
A–E · 313 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6ODH · BH3 domain swapped dimer of a BAK fragment · the same entry in another collection · chain F against F, TM-score 1.00
Q16611 · AlphaFold monomer V2.0 prediction for BCL-2 homologous ANTAGONIST/KILLER (Q16611) · a predicted model of the same protein · chain E against A, TM-score 0.72

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 6ODH · PDBe 6ODH · UniProt Q16611

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