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Cryo-EM of self-assembly peptide filament LRV_M3DELTA1

Analyse Cryo-EM of self-assembly peptide filament LRV_M3DELTA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HQE
Type: protein
Length: 1,196 residues
Chains: 52
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide LRV_M3DELTA1
Pockets: 4 · best druggability 0.34

Structure

electron microscopy · 1 distinct chain · 61% helix, 0% 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, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z	Peptide LRV_M3DELTA1	protein	23	61% helix, 0% strand	—

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.34	0.75	24	empty
2	68	0.29	0.74	19	empty
3	67	0.29	0.74	23	empty
4	51	0.27	0.75	15	empty

Interfaces

156 interfaces between chains.

o–q · 541 Å² buried · 3 hydrogen bonds · protein-protein
h–j · 540 Å² buried · 3 hydrogen bonds · protein-protein
L–N · 540 Å² buried · 5 hydrogen bonds · protein-protein
E–G · 540 Å² buried · 3 hydrogen bonds · protein-protein
f–h · 540 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6HQE · Cryo-EM of self-assembly peptide filament LRV_M3delta1 · the same entry in another collection · chain B against B, 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
Elsewhere: RCSB PDB 6HQE · PDBe 6HQE

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