Research workbench

Crystal structure of a co-bound RIDC1 variant

Analyse Crystal structure of a co-bound RIDC1 variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SU2
Type: protein
Length: 424 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble cytochrome B562
UniProt: P0ABE7
Ligands: HEC, CO
Pockets: 6 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, A, C, G	Soluble cytochrome B562	protein	106	80% helix, 0% strand	P0ABE7

Ligands and binding sites

HEC · Heme C · ligand · 4 copies · chains D, A, C, G
CO · Cobalt (II) ion · metal · 4 copies · chains D, A, C, G

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1095	0.86	0.87	142	HEC
2	147	0.57	0.82	23	HEC
3	168	0.57	0.81	26	HEC
4	97	0.39	0.76	19	empty
5	69	0.39	0.79	15	empty

Interfaces

6 interfaces between chains.

A–G · 626 Å² buried · 10 hydrogen bonds · protein-protein
D–C · 549 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 358 Å² buried · 1 hydrogen bond · protein-protein
D–G · 306 Å² buried · 1 hydrogen bond · protein-protein
C–G · 140 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 cofactor, 2 disulfide (heme c attachment, disulfide).

Compared structures

7SU2 · Crystal structure of a Co-bound RIDC1 variant · the same entry in another collection · chain G against G, TM-score 1.00
P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P0ABE7
Elsewhere: RCSB PDB 7SU2 · PDBe 7SU2 · UniProt P0ABE7

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