MolNFT v1 · #186982 · protein

Crystal structure of a metal-free RIDC1 variant

7RWV · Soluble cytochrome B562: “Crystal structure of a metal-free RIDC1 variant”. X-ray diffraction, 1 ligand (HEC), 6 pockets (best druggability 0.77). MolNFT v1 #186982 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7RWV
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
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Soluble cytochrome B562	protein	106	78% helix, 0% strand	P0ABE7

Ligands and binding sites

HEC · Heme C · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	378	0.77	0.87	68	HEC
2	349	0.74	0.85	52	HEC
3	241	0.72	0.87	45	HEC
4	76	0.72	0.96	20	empty
5	56	0.70	0.98	17	empty

Interfaces

6 interfaces between chains.

B–D · 828 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 782 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 751 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 728 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 267 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 cofactor, 2 disulfide (heme c attachment, disulfide).

Compared structures

7RWV · Crystal structure of a metal-free 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 B 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 7RWV · PDBe 7RWV · UniProt P0ABE7

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