MolNFT v1 · #15455 · protein

Crystal structure of the murine class I major histocompatibility complex of H-2DB, B2-microglobulin, and a 9-residue immunodominant peptide epitope GP33 derived from lcmv

1N5A · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of the murine class I major histocompatibility complex of H-2DB, B2-microglobulin, and a…”. X-ray diffraction, 19 pockets (best druggability 0.68). MolNFT…

PDB: 1N5A
Type: protein
Length: 1,527 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; Nonameric…
UniProt: P01899, P01887, Q9QDK7
Pockets: 19 · best druggability 0.68

Structure

x-ray diffraction · 6 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	276	25% helix, 38% strand	P01899
B	Beta-2-microglobulin	protein	98	0% helix, 52% strand	P01887
C, F, I, L	Nonameric peptide, GP33 derived from lymphocytic choriomeningitis virus	protein	9	0% helix, 0% strand	Q9QDK7
D	H-2 class I histocompatibility antigen, D-B alpha chain	protein	274	24% helix, 40% strand	P01899
E, H, K	Beta-2-microglobulin	protein	99	0% helix, 52% strand	P01887
G, J	H-2 class I histocompatibility antigen, D-B alpha chain	protein	273	26% helix, 40% strand	P01899

Pockets

19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	568	0.68	0.78	64	empty
2	687	0.67	0.76	58	empty
3	641	0.66	0.76	59	empty
4	441	0.65	0.78	41	empty
5	213	0.53	0.77	35	empty

Interfaces

10 interfaces between chains.

J–K · 1355 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1344 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1336 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1200 Å² buried · 19 hydrogen bonds · protein-protein
D–F · 950 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

1N5A · Crystal structure of the Murine class I Major Histocompatibility Complex of H-2DB… · 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
Every structure of UniProt Q9QDK7
Elsewhere: RCSB PDB 1N5A · PDBe 1N5A · UniProt P01899 · UniProt P01887 · UniProt Q9QDK7

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