MolNFT v1 · #126203 · protein

Structure of hu protein from lactococcus lactis

5LVT · DNA-binding protein hu: “Structure of hu protein from lactococcus lactis”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.76). MolNFT v1 #126203 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LVT
Type: protein
Length: 364 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-binding protein hu
UniProt: Q9CI64
Ligands: SO4
Pockets: 1 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA-binding protein hu	protein	91	43% helix, 31% strand	Q9CI64

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains B, C, A, D
ACT · Acetate ion · additive · 17 copies · chains A, C, D, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	277	0.76	0.88	43	ACT

Interfaces

6 interfaces between chains.

A–C · 2128 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 2094 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 431 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 327 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 168 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5LVT · Structure of HU protein from Lactococcus lactis · the same entry in another collection · chain D against D, TM-score 1.00
Q9CI64 · AlphaFold monomer V2.0 prediction for DNA-binding protein hu (Q9CI64) · a predicted model of the same protein · chain B against A, TM-score 0.92

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 Q9CI64
Elsewhere: RCSB PDB 5LVT · PDBe 5LVT · UniProt Q9CI64

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