GL1X · GenesisL1 explorer

MolNFT v1 · #191444 · protein + DNA

Open state of RFC:PCNA bound to a 3' SS/DSDNA junction (DNA2) with ntd

8DR5 · Replication factor C subunit 1: “Open state of RFC:PCNA bound to a 3' SS/DSDNA junction (DNA2) with ntd”. Electron microscopy, 3 ligands (AGS, GDP, MG), 20 pockets (best druggability 0.87). MolNFT v1 #191444 on GenesisL1: 3D…

PDB
8DR5
Type
protein + DNA
Length
2,798 residues
Chains
12
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Replication factor C subunit 1; Replication factor C subunit 4; Replication factor C…
UniProt
P38630, P40339, P38629, P40348, P38251, A0A6B7JGY6
Ligands
AGS, GDP, MG
Pockets
20 · best druggability 0.87

Structure

electron microscopy · 12 distinct chains · 46% helix, 19% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AReplication factor C subunit 1protein64655% helix, 8% strandP38630
BReplication factor C subunit 4protein31861% helix, 9% strandP40339
CReplication factor C subunit 3protein33060% helix, 9% strandP38629
DReplication factor C subunit 2protein33257% helix, 9% strandP40348
EReplication factor C subunit 5protein35255% helix, 13% strandP38251
FProliferating cell nuclear antigenprotein25719% helix, 46% strandA0A6B7JGY6
GProliferating cell nuclear antigenprotein25619% helix, 43% strandA0A6B7JGY6
HProliferating cell nuclear antigenprotein25818% helix, 39% strandA0A6B7JGY6
IDNA (5'-D(P*TP*TP*TP*CP*GP*GP*GP*GP*GP*GP*GP*CP*C)-3')dna13——
JDNA (5'-D(P*GP*GP*CP*CP*CP*CP*CP*CP*CP*GP*GP*C)-3')dna12——
KDNA (5'-D(P*AP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')dna11——
LDNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*TP*TP*T)-3')dna13——

Ligands and binding sites

  • AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D, E
  • GDP · Guanosine-5'-diphosphate · ligand · chains A, E
  • MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
18900.870.89104GDP
25970.840.8972empty
32160.820.9540MG, AGS
41680.810.9731MG, AGS
59720.810.8367empty

Interfaces

32 interfaces between chains.

  • A–E · 2989 Ų buried · 36 hydrogen bonds · protein-protein
  • D–E · 2735 Ų buried · 35 hydrogen bonds · protein-protein
  • B–C · 2636 Ų buried · 35 hydrogen bonds · protein-protein
  • C–D · 2557 Ų buried · 29 hydrogen bonds · protein-protein
  • A–B · 2479 Ų buried · 39 hydrogen bonds · protein-protein

Compared structures

  • P40348 · AlphaFold monomer V2.0 prediction for replication factor C subunit 2 (P40348) · a predicted model of the same protein · chain D against A, TM-score 0.96
  • P38251 · AlphaFold monomer V2.0 prediction for replication factor C subunit 5 (P38251) · a predicted model of the same protein · chain E against A, TM-score 0.95
  • P38629 · AlphaFold monomer V2.0 prediction for replication factor C subunit 3 (P38629) · a predicted model of the same protein · chain C against A, TM-score 0.91
  • P40339 · AlphaFold monomer V2.0 prediction for replication factor C subunit 4 (P40339) · a predicted model of the same protein · chain B against A, TM-score 0.83
  • P38630 · AlphaFold monomer V2.0 prediction for replication factor C subunit 1 (P38630) · a predicted model of the same protein · chain A against A, TM-score 0.55

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.