MolNFT v1 · #163715 · protein

Cryoem structure of murine perforin-2 ectodomain in a pore form

6SB5 · Macrophage-expressed gene 1 protein: “Cryoem structure of murine perforin-2 ectodomain in a pore form”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.81). MolNFT v1 #163715 on GenesisL1: 3D structure, binding…

PDB: 6SB5
Type: protein
Length: 8,688 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Macrophage-expressed gene 1 protein
UniProt: A1L314
Ligands: NAG
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 1 distinct chain · 12% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	Macrophage-expressed gene 1 protein	protein	543	12% helix, 31% strand	A1L314

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P

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

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	1005	0.81	0.82	127	empty
2	748	0.81	0.84	106	empty
3	975	0.81	0.82	112	empty
4	1098	0.81	0.82	132	empty
5	1067	0.80	0.82	123	empty

Interfaces

16 interfaces between chains.

H–I · 3876 Å² buried · 68 hydrogen bonds · protein-protein
L–M · 3781 Å² buried · 60 hydrogen bonds · protein-protein
E–F · 3778 Å² buried · 63 hydrogen bonds · protein-protein
F–G · 3760 Å² buried · 61 hydrogen bonds · protein-protein
O–P · 3756 Å² buried · 59 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 glycan, 16 disulfide (N-glycosylation, disulfide).

Compared structures

6SB5 · CryoEM structure of murine perforin-2 ectodomain in a pore form · the same entry in another collection · chain P against P, 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 A1L314
Elsewhere: RCSB PDB 6SB5 · PDBe 6SB5 · UniProt A1L314

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