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Dlp-1 from bacillus anthracis

Analyse Dlp-1 from bacillus anthracis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JI5
Type: protein
Length: 568 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dlp-1
UniProt: Q8RPQ2
Ligands: FE
Pockets: 4 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Dlp-1	protein	142	80% helix, 0% strand	Q8RPQ2

Ligands and binding sites

FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	74	0.35	0.76	14	empty
2	71	0.32	0.75	16	empty
3	66	0.29	0.73	13	empty
4	63	0.28	0.73	16	empty

Interfaces

4 interfaces between chains.

C–D · 1266 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1260 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 464 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 413 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1JI5 · Dlp-1 from bacillus anthracis · the same entry in another collection · chain D against D, TM-score 1.00
Q8RPQ2 · AlphaFold monomer V2.0 prediction for DNA protection during starvation protein 2 (Q8RPQ2) · a predicted model of the same protein · chain D 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 Q8RPQ2
Elsewhere: RCSB PDB 1JI5 · PDBe 1JI5 · UniProt Q8RPQ2

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