MolNFT v1 · #139895 · protein + RNA

Crystal structure of PHORPP38 bound to a K-turn in P12.2 helix

5XTM · 50S ribosomal protein L7AE: “Crystal structure of PHORPP38 bound to a K-turn in P12.2 helix”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.76). MolNFT v1 #139895 on GenesisL1: 3D structure, binding sites and…

PDB: 5XTM
Type: protein + RNA
Length: 338 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L7AE; RNA (47-mer)
UniProt: P62009
Ligands: MG
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	50S ribosomal protein L7AE	protein	121	50% helix, 16% strand	P62009
B, D	RNA (47-mer)	rna	47	—	—
C	50S ribosomal protein L7AE	protein	123	50% helix, 15% strand	P62009

Ligands and binding sites

MG · Magnesium ion · metal · 24 copies · chains A, B, C, D

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

Pockets

3 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	565	0.76	0.84	46	MG
2	298	0.69	0.85	27	empty
3	60	0.36	0.79	17	empty

Interfaces

5 interfaces between chains.

B–D · 785 Å² buried · 44 hydrogen bonds · nucleic-nucleic
C–D · 665 Å² buried · 25 hydrogen bonds · protein-nucleic
A–B · 628 Å² buried · 26 hydrogen bonds · protein-nucleic
A–D · 199 Å² buried · 4 hydrogen bonds · protein-nucleic
B–C · 124 Å² buried · 2 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

5XTM · Crystal structure of PhoRpp38 bound to a K-turn in P12.2 helix · the same entry in another collection · chain A against A, TM-score 1.00
P62009 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (P62009) · 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 P62009
Elsewhere: RCSB PDB 5XTM · PDBe 5XTM · UniProt P62009

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