MolNFT v1 · #15400 · protein

Crystal structure of a mycobacterial HSP60 epitope with the murine class I MHC molecule H-2DB

1N3N · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of a mycobacterial HSP60 epitope with the murine class I MHC molecule H-2DB”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.67). MolNFT…

PDB: 1N3N
Type: protein
Length: 1,540 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin…
UniProt: P01899, P01887
Ligands: SO4
Pockets: 20 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	H-2 class I histocompatibility antigen, D-B alpha chain	protein	276	24% helix, 39% strand	P01899
B, D, F, H	Beta-2-microglobulin	protein	99	0% helix, 47% strand	P01887
I, J, K, L	Mycobacterial HSP60 decameric epitope	protein	10	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains E, G

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

Pockets

20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	541	0.67	0.77	70	empty
2	528	0.65	0.77	60	empty
3	666	0.65	0.75	68	empty
4	639	0.64	0.75	54	empty
5	106	0.45	0.79	19	SO4

Interfaces

9 interfaces between chains.

E–F · 1265 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1252 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 1251 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1226 Å² buried · 19 hydrogen bonds · protein-protein
G–L · 817 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

1N3N · Crystal structure of a mycobacterial hsp60 epitope with the murine class I MHC molecule… · the same entry in another collection · chain L against L, TM-score 1.00

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 P01899
Every structure of UniProt P01887
Elsewhere: RCSB PDB 1N3N · PDBe 1N3N · UniProt P01899 · UniProt P01887

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