MolNFT v1 · #13170 · protein

Structure of the plant transcriptional regulator pbf-2

1L3A · P24: plant transcriptional regulator pbf-2: “Structure of the plant transcriptional regulator pbf-2”. X-ray diffraction, 7 pockets (best druggability 0.76). MolNFT v1 #13170 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1L3A
Type: protein
Length: 689 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: P24: plant transcriptional regulator pbf-2
UniProt: Q9LL85
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	P24: plant transcriptional regulator pbf-2	protein	166	22% helix, 43% strand	Q9LL85
B	P24: plant transcriptional regulator pbf-2	protein	170	20% helix, 43% strand	Q9LL85
C	P24: plant transcriptional regulator pbf-2	protein	182	21% helix, 41% strand	Q9LL85
D	P24: plant transcriptional regulator pbf-2	protein	171	23% helix, 43% strand	Q9LL85

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	807	0.76	0.80	83	empty
2	129	0.39	0.74	30	empty
3	119	0.37	0.73	25	empty
4	68	0.36	0.78	17	empty
5	94	0.34	0.74	23	empty

Interfaces

6 interfaces between chains.

B–C · 2016 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1595 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1490 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 1199 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 133 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1L3A · Structure of the plant transcriptional regulator PBF-2 · the same entry in another collection · chain D against D, TM-score 1.00
Q9LL85 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein WHY1… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9LL85
Elsewhere: RCSB PDB 1L3A · PDBe 1L3A · UniProt Q9LL85

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