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A de novo designed nonameric coiled coil, cc-TYPE2-(GGLAID)4

Analyse A de novo designed nonameric coiled coil, cc-TYPE2-(GGLAID)4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BIM
Type: protein
Length: 1,071 residues
Chains: 36
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nonameric de novo coiled coil cc-TYPE2-(GGLAID)4
Ligands: ACE
Pockets: 13 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 93% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, H, I, J, K, L, M, P, R, S, T, U, W, X, Y, Z, a, c, d, e, f, g, i, j	Nonameric de novo coiled coil cc-TYPE2-(GGLAID)4	protein	30	93% helix, 0% strand	—
E, G, N, O, Q, V, b	Nonameric de novo coiled coil cc-TYPE2-(GGLAID)4	protein	29	93% helix, 0% strand	—
h	Nonameric de novo coiled coil cc-TYPE2-(GGLAID)4	protein	28	93% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 36 copies · chains A, B, C, D, E, F, G, H, I, J, R, K, L, M, N, O, P, Q, S, T, U, V, W, X, Y, Z, a, b, j, c, d, e, f, g, h, i
GOL · Glycerol · additive · 39 copies · chains A, B, I, E, F, H, J, K, L, R, M, N, O, P, S, T, U, Y, Z, c, d, e, f, h, g, i
IPA · Isopropyl alcohol · additive · 7 copies · chains E, F, D, M, N, O, J, R, f, g, i

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

Pockets

13 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	834	0.85	0.85	55	GOL, IPA
2	834	0.85	0.85	57	GOL
3	784	0.84	0.85	59	GOL, IPA
4	759	0.84	0.85	53	GOL, IPA
5	448	0.81	0.88	40	empty

Interfaces

61 interfaces between chains.

e–f · 869 Å² buried · 3 hydrogen bonds · protein-protein
T–U · 860 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 857 Å² buried · 3 hydrogen bonds · protein-protein
f–g · 850 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 849 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 covalent (covalent ligand).

Compared structures

7BIM · A de novo designed nonameric coiled coil, CC-Type2-(GgLaId)4 · 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 7BIM · PDBe 7BIM

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