MolNFT v1 · #14571 · protein + DNA

Inhibited fragment of ets-1 and paired domain of PAX5 bound to DNA

1MDM · PAX5/ETS binding site on the mb-1 promoter: “Inhibited fragment of ets-1 and paired domain of PAX5 bound to DNA”. X-ray diffraction, 6 pockets (best druggability 0.72). MolNFT v1 #14571 on GenesisL1: 3D structure, binding sites and…

PDB: 1MDM
Type: protein + DNA
Length: 305 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PAX5/ETS binding site on the mb-1 promoter; Paired box protein pax-5; C-ets-1 protein
UniProt: Q02548, P27577
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	PAX5/ETS binding site on the mb-1 promoter	dna	26	—	—
D	PAX5/ETS binding site on the mb-1 promoter	dna	26	—	—
A	Paired box protein pax-5	protein	124	52% helix, 2% strand	Q02548
B	C-ets-1 protein	protein	129	44% helix, 9% strand	P27577

Pockets

6 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	145	0.72	0.91	28	empty
2	309	0.61	0.79	34	empty
3	65	0.34	0.77	14	empty
4	67	0.32	0.76	17	empty
5	50	0.31	0.78	12	empty

Interfaces

6 interfaces between chains.

C–D · 1147 Å² buried · 113 hydrogen bonds · nucleic-nucleic
D–A · 1056 Å² buried · 15 hydrogen bonds · protein-nucleic
C–A · 945 Å² buried · 26 hydrogen bonds · protein-nucleic
D–B · 491 Å² buried · 9 hydrogen bonds · protein-nucleic
C–B · 446 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

1MDM · Inhibited fragment of ets-1 and paired domain of PAX5 bound to DNA · the same entry in another collection · chain C against C, TM-score 1.00
P27577 · AlphaFold monomer V2.0 prediction for protein C-ets-1 (P27577) · a predicted model of the same protein · chain B against A, TM-score 0.96
Q02548 · AlphaFold monomer V2.0 prediction for paired box protein pax-5 (Q02548) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q02548
Every structure of UniProt P27577
Elsewhere: RCSB PDB 1MDM · PDBe 1MDM · UniProt Q02548 · UniProt P27577

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