MolNFT v1 · #167260 · protein

Gasdermin D pore

6VFE · Gasdermin-D, N-terminal: “Gasdermin D pore”. Electron microscopy, 20 pockets (best druggability 0.80). MolNFT v1 #167260 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VFE
Type: protein
Length: 7,887 residues
Chains: 33
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gasdermin-D, N-terminal
UniProt: P57764
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 1 distinct chain · 12% helix, 45% 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, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g	Gasdermin-D, N-terminal	protein	239	12% helix, 45% strand	P57764

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	143	0.80	0.97	44	empty
2	158	0.80	0.96	39	empty
3	127	0.80	0.97	33	empty
4	138	0.79	0.96	24	empty
5	135	0.79	0.96	31	empty

Interfaces

33 interfaces between chains.

T–U · 1972 Å² buried · 33 hydrogen bonds · protein-protein
J–K · 1972 Å² buried · 32 hydrogen bonds · protein-protein
Z–a · 1969 Å² buried · 36 hydrogen bonds · protein-protein
E–F · 1955 Å² buried · 28 hydrogen bonds · protein-protein
f–g · 1955 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

P57764 · AlphaFold monomer V2.0 prediction for gasdermin-D (P57764) · a predicted model of the same protein · chain H against A, TM-score 0.90

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 P57764
Elsewhere: RCSB PDB 6VFE · PDBe 6VFE · UniProt P57764

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