MolNFT v1 · #116412 · protein + RNA

Crystal structure of PHORPP38-SL12M complex

5DCV · 50S ribosomal protein L7AE: “Crystal structure of PHORPP38-SL12M complex”. X-ray diffraction, 6 pockets (best druggability 0.53). MolNFT v1 #116412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DCV
Type: protein + RNA
Length: 330 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
Pockets: 6 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	50S ribosomal protein L7AE	protein	118	52% helix, 14% strand	P62009
B, D	RNA (47-mer)	rna	47	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	339	0.53	0.75	18	empty
2	309	0.51	0.74	17	empty
3	169	0.50	0.78	22	empty
4	70	0.30	0.74	13	empty
5	57	0.28	0.74	14	empty

Interfaces

5 interfaces between chains.

B–D · 698 Å² buried · 40 hydrogen bonds · nucleic-nucleic
A–B · 615 Å² buried · 18 hydrogen bonds · protein-nucleic
C–D · 575 Å² buried · 16 hydrogen bonds · protein-nucleic
B–C · 142 Å² buried · 2 hydrogen bonds · protein-nucleic
A–D · 133 Å² buried · 3 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

5DCV · Crystal structure of PhoRpp38-SL12M complex · 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 0.98

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 5DCV · PDBe 5DCV · UniProt P62009

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