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Crystal structure of a zn-bound RIDC1 variant

Analyse Crystal structure of a zn-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: 7RWW
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, ZN
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Soluble cytochrome B562	protein	106	79% helix, 0% strand	P0ABE7

Ligands and binding sites

HEC · Heme C · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 5 copies · chains A, D, B, C
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains B, D, A, C
MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, C
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	714	0.83	0.87	78	MPD, EPE, ZN
2	317	0.75	0.87	36	MRD
3	137	0.58	0.83	22	HEC
4	145	0.57	0.82	22	HEC
5	137	0.55	0.81	21	HEC

Interfaces

6 interfaces between chains.

A–B · 589 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 578 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 452 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 422 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 124 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor, 2 disulfide (heme c attachment, disulfide).

Compared structures

7RWW · Crystal structure of a Zn-bound RIDC1 variant · the same entry in another collection · chain D against D, TM-score 1.00
P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 7RWW · PDBe 7RWW · UniProt P0ABE7

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