MolNFT v1 · #56862 · protein

Crystal structure of H-2KB in complex with the Q600Y variant of jhmv epitope S598

2ZSW · H-2 class I histocompatibility antigen, K-B alpha chain: “Crystal structure of H-2KB in complex with the Q600Y variant of jhmv epitope S598”. X-ray diffraction, 15 pockets (best druggability 0.64). MolNFT v1 #56862 on GenesisL1: 3D…

PDB: 2ZSW
Type: protein
Length: 1,532 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; 8-mer…
UniProt: P01901, P01887
Pockets: 15 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, C, G	H-2 class I histocompatibility antigen, K-B alpha chain	protein	277	27% helix, 39% strand	P01901
H, F, B, D	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P01887
M, N, O, P	8-mer peptide from spike glycoprotein	protein	8	0% helix, 0% strand	—

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	596	0.64	0.75	55	empty
2	492	0.63	0.76	60	empty
3	507	0.62	0.75	50	empty
4	498	0.62	0.75	46	empty
5	488	0.60	0.74	47	empty

Interfaces

14 interfaces between chains.

C–D · 1197 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1171 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1165 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1156 Å² buried · 20 hydrogen bonds · protein-protein
E–N · 873 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 modified (disulfide, nonstandard).

Compared structures

2ZSW · Crystal structure of H-2Kb in complex with the Q600Y variant of JHMV epitope S598 · the same entry in another collection · chain P against P, 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 P01901
Every structure of UniProt P01887
Elsewhere: RCSB PDB 2ZSW · PDBe 2ZSW · UniProt P01901 · UniProt P01887

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