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Endophilin B1 helical scaffold

Analyse Endophilin B1 helical scaffold in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UPN
Type: protein
Length: 11,760 residues
Chains: 48
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endophilin-B1
UniProt: Q9Y371
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 65% 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, V, W, X, Y, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, v, w, x, y	Endophilin-B1	protein	245	65% helix, 0% strand	Q9Y371

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	319	0.85	0.95	48	empty
2	319	0.85	0.94	50	empty
3	318	0.85	0.94	51	empty
4	334	0.85	0.94	51	empty
5	316	0.85	0.94	49	empty

Interfaces

100 interfaces between chains.

X–Y · 3241 Å² buried · 18 hydrogen bonds · protein-protein
g–h · 3240 Å² buried · 18 hydrogen bonds · protein-protein
k–l · 3238 Å² buried · 18 hydrogen bonds · protein-protein
S–T · 3236 Å² buried · 18 hydrogen bonds · protein-protein
s–t · 3236 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

6UPN · Endophilin B1 helical scaffold · 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
Every structure of UniProt Q9Y371
Elsewhere: RCSB PDB 6UPN · PDBe 6UPN · UniProt Q9Y371

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