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Crystal structure of human bak in complex with wt bak BH3 peptide

Analyse Crystal structure of human bak in complex with wt bak BH3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7M5C
Type: protein
Length: 1,688 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2 homologous ANTAGONIST/KILLER
UniProt: Q16611
Ligands: CU, SO4
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 16 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2 homologous ANTAGONIST/KILLER	protein	151	77% helix, 0% strand	Q16611
B, H, L, P	BCL-2 homologous ANTAGONIST/KILLER	protein	22	82% helix, 0% strand	Q16611
C	BCL-2 homologous ANTAGONIST/KILLER	protein	151	75% helix, 0% strand	Q16611
D	BCL-2 homologous ANTAGONIST/KILLER	protein	17	82% helix, 0% strand	Q16611
E	BCL-2 homologous ANTAGONIST/KILLER	protein	157	75% helix, 0% strand	Q16611
F	BCL-2 homologous ANTAGONIST/KILLER	protein	24	75% helix, 0% strand	Q16611
G	BCL-2 homologous ANTAGONIST/KILLER	protein	139	78% helix, 0% strand	Q16611
I	BCL-2 homologous ANTAGONIST/KILLER	protein	145	75% helix, 0% strand	Q16611
J	BCL-2 homologous ANTAGONIST/KILLER	protein	20	80% helix, 0% strand	Q16611
K	BCL-2 homologous ANTAGONIST/KILLER	protein	147	77% helix, 0% strand	Q16611
M	BCL-2 homologous ANTAGONIST/KILLER	protein	149	77% helix, 0% strand	Q16611
N, R	BCL-2 homologous ANTAGONIST/KILLER	protein	19	89% helix, 0% strand	Q16611
O	BCL-2 homologous ANTAGONIST/KILLER	protein	151	75% helix, 0% strand	Q16611
Q	BCL-2 homologous ANTAGONIST/KILLER	protein	147	77% helix, 0% strand	Q16611
S	BCL-2 homologous ANTAGONIST/KILLER	protein	143	73% helix, 0% strand	Q16611
T	BCL-2 homologous ANTAGONIST/KILLER	protein	21	86% helix, 0% strand	Q16611

Ligands and binding sites

CU · Copper (II) ion · metal · 9 copies · chains A, M, C, O, E, G, I, Q, S
SO4 · Sulfate ion · ion · 8 copies · chains A, G, H, M, P, T

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	865	0.74	0.79	94	empty
2	558	0.69	0.78	58	empty
3	380	0.68	0.80	30	empty
4	749	0.67	0.75	78	empty
5	306	0.62	0.79	34	empty

Interfaces

29 interfaces between chains.

E–F · 1065 Å² buried · 12 hydrogen bonds · protein-protein
O–P · 1028 Å² buried · 8 hydrogen bonds · protein-protein
K–L · 1002 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 976 Å² buried · 10 hydrogen bonds · protein-protein
M–N · 965 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7M5C · Crystal Structure of human BAK in complex with WT BAK BH3 peptide · the same entry in another collection · chain G against G, 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 7M5C · PDBe 7M5C · UniProt Q16611

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