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MolNFT v2 · #194621 · protein

Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity

7ST3 · Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen…: “Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity”. X-ray diffraction at 2.78, 20 pockets (best druggability 0.68). MolNFT…

PDB
7ST3
Type
protein
Length
7,611 residues
Chains
32
Method
x-ray diffraction
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
2.78
Source
Homo sapiens; Human papillomavirus type 16; Lama glama; Pongo pygmaeus
Molecule
Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera; Vhh
UniProt
P03129, P16213, A0A678ZGP6
Pockets
20 · best druggability 0.68

Structure

x-ray diffraction · resolution 2.78 · 17 distinct chains · 20% helix, 41% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein35220% helix, 40% strandP03129, P16213, A0A678ZGP6
B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d, fVhhprotein1155% helix, 50% strand—
CProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein36120% helix, 41% strandP03129, P16213, A0A678ZGP6
EProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein36819% helix, 41% strandP03129, P16213, A0A678ZGP6
GProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein36620% helix, 41% strandP03129, P16213, A0A678ZGP6
IProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein35820% helix, 41% strandP03129, P16213, A0A678ZGP6
KProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein37620% helix, 40% strandP03129, P16213, A0A678ZGP6
MProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein37219% helix, 41% strandP03129, P16213, A0A678ZGP6
OProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein36120% helix, 41% strandP03129, P16213, A0A678ZGP6
QProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein37520% helix, 42% strandP03129, P16213, A0A678ZGP6
SProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein34520% helix, 39% strandP03129, P16213, A0A678ZGP6
UProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein34821% helix, 41% strandP03129, P16213, A0A678ZGP6
WProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein35020% helix, 40% strandP03129, P16213, A0A678ZGP6
YProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein37620% helix, 42% strandP03129, P16213, A0A678ZGP6
aProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein35720% helix, 39% strandP03129, P16213, A0A678ZGP6
cProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein35220% helix, 40% strandP03129, P16213, A0A678ZGP6
eProtein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimeraprotein35420% helix, 41% strandP03129, P16213, A0A678ZGP6

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
16230.680.7756empty
25760.680.7862empty
35080.680.7850empty
45890.680.7756empty
56150.670.7758empty

Interfaces

52 interfaces between chains.

  • c–d · 929 Ų buried · 18 hydrogen bonds · protein-protein
  • M–N · 927 Ų buried · 20 hydrogen bonds · protein-protein
  • I–J · 925 Ų buried · 15 hydrogen bonds · protein-protein
  • O–P · 924 Ų buried · 16 hydrogen bonds · protein-protein
  • G–H · 923 Ų buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 79 disulfide (disulfide).

Compared structures

  • P16213 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P16213) · a predicted model of the same protein · chain S against A, TM-score 0.28

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