MolNFT v1 · #87558 · protein + RNA

Structure of a rare, non-standard sequence K-turn bound by L7AE protein

4C4W · U1 small nuclear ribonucleoprotein a: “Structure of a rare, non-standard sequence K-turn bound by L7AE protein”. X-ray diffraction, 1 ligand (2HP), 11 pockets (best druggability 0.70). MolNFT v1 #87558 on GenesisL1: 3D structure…

PDB: 4C4W
Type: protein + RNA
Length: 686 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U1 small nuclear ribonucleoprotein a; 50S ribosomal protein L7AE; Tskt-23
UniProt: P09012, O29494
Ligands: 2HP
Pockets: 11 · best druggability 0.70

Structure

x-ray diffraction · 7 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	U1 small nuclear ribonucleoprotein a	protein	96	31% helix, 23% strand	P09012
B	U1 small nuclear ribonucleoprotein a	protein	95	35% helix, 25% strand	P09012
C	50S ribosomal protein L7AE	protein	115	44% helix, 17% strand	O29494
D, H	Tskt-23	rna	35	—	—
E	U1 small nuclear ribonucleoprotein a	protein	97	33% helix, 23% strand	P09012
F	U1 small nuclear ribonucleoprotein a	protein	96	34% helix, 27% strand	P09012
G	50S ribosomal protein L7AE	protein	117	44% helix, 14% strand	—

Ligands and binding sites

2HP · Dihydrogenphosphate ion · ion · 2 copies · chains D, H

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

Pockets

11 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	836	0.70	0.76	80	empty
2	326	0.55	0.76	31	empty
3	100	0.44	0.79	16	empty
4	182	0.41	0.72	20	empty
5	92	0.40	0.77	20	empty

Interfaces

13 interfaces between chains.

E–H · 946 Å² buried · 32 hydrogen bonds · protein-nucleic
A–D · 898 Å² buried · 28 hydrogen bonds · protein-nucleic
C–D · 626 Å² buried · 20 hydrogen bonds · protein-nucleic
E–F · 626 Å² buried · 2 hydrogen bonds · protein-protein
G–H · 621 Å² buried · 21 hydrogen bonds · protein-nucleic

Compared structures

4C4W · Structure of a rare, non-standard sequence k-turn bound by L7Ae protein · the same entry in another collection · chain H against H, TM-score 1.00
O29494 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (O29494) · a predicted model of the same protein · chain C 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 P09012
Every structure of UniProt O29494
Elsewhere: RCSB PDB 4C4W · PDBe 4C4W · UniProt P09012 · UniProt O29494

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