MolNFT v1 · #14153 · protein

HLA B8 in complex with an epstein barr virus determinant

1M05 · HLA class I histocompatibility antigen, B-8 B*0801 alpha…: “HLA B8 in complex with an epstein barr virus determinant”. X-ray diffraction, 1 ligand (CD), 8 pockets (best druggability 0.67). MolNFT v1 #14153 on GenesisL1: 3D…

PDB: 1M05
Type: protein
Length: 754 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-8 B*0801 alpha chain; Beta-2-microglobulin…
UniProt: P30460, P61769, P12977
Ligands: CD
Pockets: 8 · best druggability 0.67

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	HLA class I histocompatibility antigen, B-8 B*0801 alpha chain	protein	269	26% helix, 39% strand	P30460
B, D	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
E, F	Ebna-3 nuclear protein	protein	9	0% helix, 0% strand	P12977

Ligands and binding sites

CD · Cadmium ion · metal · 2 copies · chains B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	584	0.67	0.77	65	empty
2	559	0.66	0.77	53	empty
3	552	0.65	0.76	48	empty
4	83	0.46	0.81	19	empty
5	76	0.45	0.81	18	empty

Interfaces

6 interfaces between chains.

A–B · 1351 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1321 Å² buried · 20 hydrogen bonds · protein-protein
C–F · 999 Å² buried · 23 hydrogen bonds · protein-protein
A–E · 995 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 192 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1M05 · HLA B8 in complex with an Epstein Barr Virus determinant · the same entry in another collection · chain F against F, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D 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 P30460
Every structure of UniProt P61769
Every structure of UniProt P12977
Elsewhere: RCSB PDB 1M05 · PDBe 1M05 · UniProt P30460 · UniProt P61769 · UniProt P12977

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