MolNFT v1 · #47536 · protein

Plasmodium yoelii ribonucleotide reductase subunit R2 (PY03671)

2P1I · Ribonucleotide reductase, small chain: “Plasmodium yoelii ribonucleotide reductase subunit R2 (PY03671)”. X-ray diffraction, 1 ligand (FE), 20 pockets (best druggability 0.82). MolNFT v1 #47536 on GenesisL1: 3D structure, binding…

PDB: 2P1I
Type: protein
Length: 2,050 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonucleotide reductase, small chain
UniProt: Q7RIF3
Ligands: FE
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E, F, H	Ribonucleotide reductase, small chain	protein	258	68% helix, 0% strand	Q7RIF3
B	Ribonucleotide reductase, small chain	protein	252	67% helix, 0% strand	Q7RIF3
C	Ribonucleotide reductase, small chain	protein	256	70% helix, 0% strand	Q7RIF3
G	Ribonucleotide reductase, small chain	protein	252	66% helix, 0% strand	Q7RIF3

Ligands and binding sites

FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1105	0.82	0.82	113	empty
2	1099	0.81	0.82	124	empty
3	849	0.76	0.79	76	empty
4	769	0.75	0.80	76	empty
5	692	0.74	0.79	57	empty

Interfaces

7 interfaces between chains.

G–H · 808 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 737 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 728 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 723 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 154 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2P1I · Plasmodium yoelii Ribonucleotide Reductase Subunit R2 (PY03671) · 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
Every structure of UniProt Q7RIF3
Elsewhere: RCSB PDB 2P1I · PDBe 2P1I · UniProt Q7RIF3

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