MolNFT v1 · #141047 · protein

Crystal structure of ssb complexed with myc

5YUN · Single-stranded DNA-binding protein: “Crystal structure of ssb complexed with myc”. X-ray diffraction, 1 ligand (MYC), 4 pockets (best druggability 0.72). MolNFT v1 #141047 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5YUN
Type: protein
Length: 411 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-stranded DNA-binding protein
UniProt: P40947
Ligands: MYC
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 62% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Single-stranded DNA-binding protein	protein	104	9% helix, 63% strand	P40947
B	Single-stranded DNA-binding protein	protein	103	9% helix, 58% strand	P40947
C	Single-stranded DNA-binding protein	protein	102	12% helix, 65% strand	P40947
D	Single-stranded DNA-binding protein	protein	102	9% helix, 64% strand	P40947

Ligands and binding sites

MYC · 3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-4H-chromen-4-one · ligand · 2 copies · chains B, C, A, D

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

Pockets

4 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	668	0.72	0.79	72	MYC
2	587	0.69	0.78	60	MYC
3	205	0.55	0.79	32	empty
4	139	0.50	0.79	29	empty

Interfaces

6 interfaces between chains.

C–D · 1289 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1006 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 346 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 312 Å² buried · 1 hydrogen bond · protein-protein
A–C · 284 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5YUN · Crystal structure of SSB complexed with myc · the same entry in another collection · chain D against D, TM-score 1.00
P40947 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein (P40947) · a predicted model of the same protein · chain D 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 P40947
Elsewhere: RCSB PDB 5YUN · PDBe 5YUN · UniProt P40947

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