MolNFT v1 · #126806 · protein

Structure of the RNA recognition motif (rrm) of SEB1 from S. pombe.

5MDU · RPB7-binding protein SEB1: “Structure of the RNA recognition motif (rrm) of SEB1 from S. pombe.”. X-ray diffraction, 2 ligands (NA, CL), 2 pockets (best druggability 0.34). MolNFT v1 #126806 on GenesisL1: 3D structure, binding sites…

PDB: 5MDU
Type: protein
Length: 153 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RPB7-binding protein SEB1
UniProt: Q9UTE3
Ligands: NA, CL
Pockets: 2 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RPB7-binding protein SEB1	protein	153	24% helix, 31% strand	Q9UTE3

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	60	0.34	0.77	12	empty
2	56	0.27	0.73	13	empty

Compared structures

5MDU · Structure of the RNA recognition motif (RRM) of Seb1 from S. pombe. · the same entry in another collection · chain A against A, TM-score 1.00
Q9UTE3 · AlphaFold monomer V2.0 prediction for RPB7-binding protein SEB1 (Q9UTE3) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9UTE3
Elsewhere: RCSB PDB 5MDU · PDBe 5MDU · UniProt Q9UTE3

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