MolNFT v1 · #74108 · protein + DNA

Crystal structure of the PED208 tram-sbma complex

3ON0 · Protein tram: “Crystal structure of the PED208 tram-sbma complex”. X-ray diffraction, 3 pockets (best druggability 0.76). MolNFT v1 #74108 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3ON0
Type: protein + DNA
Length: 488 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein tram; Sbma
UniProt: P33788
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 76% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein tram	protein	121	75% helix, 4% strand	P33788
B, C	Protein tram	protein	118	76% helix, 4% strand	P33788
D	Protein tram	protein	107	77% helix, 5% strand	P33788
P	Sbma	dna	24	—	—

Pockets

3 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	95	0.76	0.98	20	empty
2	151	0.65	0.87	20	empty
3	303	0.60	0.78	35	empty

Interfaces

10 interfaces between chains.

B–C · 2974 Å² buried · 26 hydrogen bonds · protein-protein
A–D · 2870 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 1398 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 1304 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 651 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3ON0 · Crystal structure of the pED208 TraM-sbmA complex · the same entry in another collection · chain P against P, TM-score 1.00
P33788 · AlphaFold monomer V2.0 prediction for relaxosome protein tram (P33788) · a predicted model of the same protein · chain D against A, TM-score 0.54

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 P33788
Elsewhere: RCSB PDB 3ON0 · PDBe 3ON0 · UniProt P33788

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