MolNFT v1 · #103794 · protein

Crystal structure of a HLA-B*35:08-hpvg-D5

4PRD · MHC class I antigen: “Crystal structure of a HLA-B*35:08-hpvg-D5”. X-ray diffraction, 3 pockets (best druggability 0.70). MolNFT v1 #103794 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PRD
Type: protein
Length: 386 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Epstein-barr nuclear antigen 1
UniProt: C5MK56, P61769, Q3KSS4
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	27% helix, 39% strand	C5MK56
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Epstein-barr nuclear antigen 1	protein	11	0% helix, 0% strand	Q3KSS4

Ligands and binding sites

ACT · Acetate ion · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	647	0.70	0.78	54	empty
2	174	0.49	0.77	31	empty
3	96	0.46	0.80	23	empty

Interfaces

2 interfaces between chains.

A–B · 1342 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 833 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4PRD · Crystal structure of a HLA-B*35:08-HPVG-D5 · the same entry in another collection · chain A against A, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt C5MK56
Every structure of UniProt P61769
Every structure of UniProt Q3KSS4
Elsewhere: RCSB PDB 4PRD · PDBe 4PRD · UniProt C5MK56 · UniProt P61769 · UniProt Q3KSS4

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