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Early B-cell factor 1 (EBF1) bound to DNA

Analyse Early B-cell factor 1 (EBF1) bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MLP
Type: protein + DNA
Length: 1,358 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription factor COE1; DNA (5'- D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*…
UniProt: Q07802
Ligands: ZN
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription factor COE1	protein	337	12% helix, 39% strand	Q07802
B	Transcription factor COE1	protein	332	11% helix, 40% strand	Q07802
C, D, G, H	DNA (5'- D(CPTPTPTPAPTPTPCPCPCPAPTPGPGPGPAPAPTPAPAPAPG)- 3')	dna	22	—	—
E	Transcription factor COE1	protein	303	10% helix, 44% strand	Q07802
F	Transcription factor COE1	protein	298	9% helix, 43% strand	Q07802

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, E, F
CIT · Citric acid · additive · 5 copies · chains A, E, F, B

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1157	0.84	0.85	82	empty
2	1191	0.83	0.84	68	empty
3	576	0.68	0.78	60	CIT
4	483	0.66	0.78	46	CIT
5	521	0.65	0.77	44	CIT

Interfaces

17 interfaces between chains.

A–B · 1579 Å² buried · 11 hydrogen bonds · protein-protein
G–H · 967 Å² buried · 96 hydrogen bonds · nucleic-nucleic
A–E · 962 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 959 Å² buried · 88 hydrogen bonds · nucleic-nucleic
E–G · 805 Å² buried · 22 hydrogen bonds · protein-nucleic

Compared structures

3MLP · Early B-cell Factor 1 (Ebf1) bound to DNA · the same entry in another collection · chain H against H, TM-score 1.00
Q07802 · AlphaFold monomer V2.0 prediction for transcription factor COE1 (Q07802) · a predicted model of the same protein · chain E against A, TM-score 0.99

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 Q07802
Elsewhere: RCSB PDB 3MLP · PDBe 3MLP · UniProt Q07802

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