MolNFT v1 · #176711 · protein

Crystal structure of the computationally designed REDPBB_SYM1 protein

7DVC: “Crystal structure of the computationally designed REDPBB_SYM1 protein”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.51). MolNFT v1 #176711 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DVC
Type: protein
Length: 522 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: REDPBB_SYM1 protein
Ligands: CL
Pockets: 5 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, F, B, D	REDPBB_SYM1 protein	protein	87	23% helix, 37% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 9 copies · chains A, C, B, E, D
ACT · Acetate ion · additive · 5 copies · chains C, F, E, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	268	0.51	0.75	36	CL
2	263	0.49	0.74	34	ACT
3	217	0.49	0.75	32	CL, ACT
4	57	0.28	0.74	15	ACT
5	66	0.28	0.73	16	empty

Interfaces

9 interfaces between chains.

A–C · 404 Å² buried · 14 hydrogen bonds · protein-protein
E–B · 403 Å² buried · 11 hydrogen bonds · protein-protein
C–F · 397 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 359 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 347 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7DVC · Crystal structure of the computationally designed reDPBB_sym1 protein · the same entry in another collection · chain A against A, 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 7DVC · PDBe 7DVC

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.