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Crystal structure of murine perforin-2 P2 domain crystal form 2

Analyse Crystal structure of murine perforin-2 P2 domain crystal form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SB4
Type: protein
Length: 1,571 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Macrophage-expressed gene 1 protein
UniProt: A1L314
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 7 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Macrophage-expressed gene 1 protein	protein	196	6% helix, 53% strand	A1L314
B	Macrophage-expressed gene 1 protein	protein	198	6% helix, 53% strand	A1L314
C, E	Macrophage-expressed gene 1 protein	protein	197	6% helix, 53% strand	A1L314
D	Macrophage-expressed gene 1 protein	protein	195	6% helix, 52% strand	A1L314
F	Macrophage-expressed gene 1 protein	protein	196	6% helix, 54% strand	A1L314
G	Macrophage-expressed gene 1 protein	protein	196	6% helix, 53% strand	A1L314
H	Macrophage-expressed gene 1 protein	protein	196	8% helix, 53% strand	A1L314

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	972	0.80	0.81	93	empty
2	818	0.79	0.82	88	empty
3	943	0.78	0.81	95	empty
4	964	0.78	0.80	92	empty
5	143	0.58	0.83	22	empty

Interfaces

11 interfaces between chains.

B–H · 890 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 660 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 596 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 588 Å² buried · 9 hydrogen bonds · protein-protein
A–G · 573 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 49 disulfide (disulfide).

Compared structures

6SB4 · Crystal structure of murine perforin-2 P2 domain crystal form 2 · the same entry in another collection · chain H against H, TM-score 1.00
A1L314 · AlphaFold monomer V2.0 prediction for macrophage-expressed gene 1 protein (A1L314) · a predicted model of the same protein · chain H against A, TM-score 0.97

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 A1L314
Elsewhere: RCSB PDB 6SB4 · PDBe 6SB4 · UniProt A1L314

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