MolNFT v1 · #12436 · protein

R2F from corynebacterium ammoniagenes in its mn substituted form

1KGP · Ribonucleotide reductase protein R2F: “R2F from corynebacterium ammoniagenes in its mn substituted form”. X-ray diffraction, 1 ligand (MN), 12 pockets (best druggability 0.56). MolNFT v1 #12436 on GenesisL1: 3D structure, binding…

PDB: 1KGP
Type: protein
Length: 1,184 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonucleotide reductase protein R2F
UniProt: O69274
Ligands: MN
Pockets: 12 · best druggability 0.56

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ribonucleotide reductase protein R2F	protein	296	78% helix, 0% strand	O69274

Ligands and binding sites

MN · Manganese (II) ion · metal · 10 copies · chains A, B, C, D

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

Pockets

12 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	124	0.56	0.83	21	empty
2	285	0.52	0.74	35	empty
3	136	0.42	0.75	18	empty
4	140	0.39	0.73	22	empty
5	73	0.37	0.77	17	empty

Interfaces

3 interfaces between chains.

C–D · 2758 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2755 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 241 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1KGP · R2F from Corynebacterium Ammoniagenes in its Mn substituted form · 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 O69274
Elsewhere: RCSB PDB 1KGP · PDBe 1KGP · UniProt O69274

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