MolNFT v1 · #50520 · protein

Structure of oppa complexed with lys-lys

2RKM · Oligo-peptide binding protein: “Structure of oppa complexed with lys-lys”. X-ray diffraction, 1 ligand (IUM), 3 pockets (best druggability 0.74). MolNFT v1 #50520 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2RKM
Type: protein
Length: 519 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oligo-peptide binding protein
UniProt: P06202
Ligands: IUM
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oligo-peptide binding protein	protein	519	34% helix, 22% strand	P06202

Ligands and binding sites

IUM · Uranyl (VI) ion · ligand · 8 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	80	0.74	0.97	29	empty
2	109	0.44	0.78	21	empty
3	71	0.30	0.74	18	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2RKM · Structure of oppa complexed with lys-lys · the same entry in another collection · chain A against A, TM-score 1.00
P06202 · AlphaFold monomer V2.0 prediction for periplasmic oligopeptide- binding protein (P06202) · a predicted model of the same protein · chain A 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 P06202
Elsewhere: RCSB PDB 2RKM · PDBe 2RKM · UniProt P06202

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