MolNFT v1 · #102216 · protein

Crystal structure of rst D1-D2

4OF8 · Irregular chiasm C-roughest protein: “Crystal structure of rst D1-D2”. X-ray diffraction, 1 ligand (NA), 9 pockets (best druggability 0.66). MolNFT v1 #102216 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4OF8
Type: protein
Length: 839 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Irregular chiasm C-roughest protein
UniProt: Q08180
Ligands: NA
Pockets: 9 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Irregular chiasm C-roughest protein	protein	211	3% helix, 50% strand	Q08180
B, D	Irregular chiasm C-roughest protein	protein	209	3% helix, 49% strand	Q08180
C	Irregular chiasm C-roughest protein	protein	210	3% helix, 49% strand	Q08180

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 6 copies · chains A, D, B

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

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	518	0.66	0.78	60	NA, GOL
2	432	0.66	0.79	48	empty
3	55	0.39	0.81	19	empty
4	122	0.35	0.72	28	empty
5	93	0.35	0.74	17	empty

Interfaces

5 interfaces between chains.

A–B · 682 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 655 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 654 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 58 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 56 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4OF8 · Crystal Structure of Rst D1-D2 · the same entry in another collection · chain A against A, TM-score 1.00
Q08180 · AlphaFold monomer V2.0 prediction for irregular chiasm C-roughest protein (Q08180) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q08180
Elsewhere: RCSB PDB 4OF8 · PDBe 4OF8 · UniProt Q08180

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