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Structural basis for a six letter alphabet including gatckx

Analyse Structural basis for a six letter alphabet including gatckx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5VBS
Type
protein + DNA
Length
262 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Reverse transcriptase catalytic fragment; DNA (5'-D(*CP*TP*TP*AP*TP*(DX)P*(DX)P*T)-3')…
EC
2.7.7.49, 2.7.7.7
UniProt
P03355
Pockets
3 · best druggability 0.42

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AReverse transcriptase catalytic fragment (EC 2.7.7.49, 2.7.7.7)protein24631% helix, 22% strandP03355
BDNA (5'-D(*CP*TP*TP*AP*TP*(DX)P*(DX)P*T)-3')dna8——
GDNA (5'-D(P*AP*(93D)P*(93D)P*AP*TP*AP*AP*G)-3')dna8——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11060.420.7822empty
2510.410.8210empty
31170.400.7517empty

Interfaces

3 interfaces between chains.

  • B–G · 354 Ų buried · 36 hydrogen bonds · nucleic-nucleic
  • A–B · 260 Ų buried · 4 hydrogen bonds · protein-nucleic
  • A–G · 205 Ų buried · 4 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

  • 5VBS · Structural basis for a six letter alphabet including GATCKX · the same entry in another collection · chain A against A, TM-score 1.00

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