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Endogenous retrovirus HML2 capsid ntd

Analyse Endogenous retrovirus HML2 capsid ntd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6SA9
Type
protein
Length
269 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Endogenous retrovirus group K member 9 pol protein
EC
3.4.23.50, 2.7.7.49, 2.7.7.7, 3.1.26.4
UniProt
P63128
Pockets
2 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 68% helix, 3% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEndogenous retrovirus group K member 9 pol protein (EC 3.4.23.50, 2.7.7.49, 2.7.7.7, 3.1.26.4)protein13567% helix, 1% strandP63128
BEndogenous retrovirus group K member 9 pol protein (EC 3.4.23.50, 2.7.7.49, 2.7.7.7, 3.1.26.4)protein13468% helix, 5% strandP63128

Ligands and binding sites

  • GOL · Glycerol · additive · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12810.610.8035empty
2530.390.8116empty

Interfaces

1 interface between chains.

  • A–B · 816 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

  • 6SA9 · Endogenous Retrovirus HML2 Capsid NTD · the same entry in another collection · chain A against A, TM-score 1.00
  • P63128 · AlphaFold monomer V2.0 prediction for endogenous retrovirus group K member 9 pol protein… · a predicted model of the same protein · chain B against A, TM-score 0.97

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