GL1X · GenesisL1 explorer

MolNFT v1 · #50582 · protein

Rmp-pepstatin a complex

2RMP · Mucoropepsin: “Rmp-pepstatin a complex”. X-ray diffraction, 3 ligands (IVA, NAG, BMA), 1 pocket (best druggability 0.32). MolNFT v1 #50582 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
2RMP
Type
protein
Length
363 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Mucoropepsin; Pepstatin
EC
3.4.23.23
UniProt
P00799
Ligands
IVA, NAG, BMA
Pockets
1 · best druggability 0.32

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 44% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AMucoropepsin (EC 3.4.23.23)protein35810% helix, 45% strandP00799
BPepstatinprotein50% helix, 0% strand—

Ligands and binding sites

  • IVA · Isovaleric acid · ligand · chains A, B
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
  • BMA · beta-D-mannopyranose · sugar

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1880.320.7319empty

Interfaces

1 interface between chains.

  • A–B · 568 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 2 glycan, 2 modified, 1 covalent (disulfide, N-glycosylation, nonstandard, covalent ligand).

Compared structures

  • 2RMP · RMP-pepstatin A complex · the same entry in another collection · chain A against A, TM-score 1.00
  • P00799 · AlphaFold monomer V2.0 prediction for mucorpepsin (P00799) · a predicted model of the same protein · chain A against A, TM-score 0.99

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