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Murine class I major histocompatibility complex H-2KB in complex with post-translationally modified lcmv-derived GP34-41 peptide, comprising a nitrotyrosine at position 3

Analyse Murine class I major histocompatibility complex H-2KB in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ROL
Type: protein
Length: 757 residues
Chains: 6
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…
UniProt: P01901, P01887, Q9QDK7
Ligands: PO4
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 23% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, K-B alpha chain	protein	271	28% helix, 40% strand	P01901
B, D	Beta-2-microglobulin	protein	99	0% helix, 55% strand	P01887
C	H-2 class I histocompatibility antigen, K-B alpha chain	protein	272	28% helix, 40% strand	P01901
E, F	Pre-glycoprotein polyprotein gp complex	protein	8	0% helix, 0% strand	Q9QDK7

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D
GOL · Glycerol · additive · chains C, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C, D

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

Pockets

10 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	1165	0.74	0.77	100	empty
2	205	0.57	0.80	31	GOL, MPD, PO4
3	222	0.57	0.79	34	PO4
4	62	0.55	0.88	18	empty
5	62	0.51	0.86	18	empty

Interfaces

5 interfaces between chains.

C–D · 1394 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1377 Å² buried · 23 hydrogen bonds · protein-protein
C–F · 858 Å² buried · 23 hydrogen bonds · protein-protein
A–E · 854 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 728 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 modified (disulfide, nonstandard).

Compared structures

3ROL · Murine class I major histocompatibility complex H-2Kb in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.97

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
Every structure of UniProt Q9QDK7
Elsewhere: RCSB PDB 3ROL · PDBe 3ROL · UniProt P01901 · UniProt P01887 · UniProt Q9QDK7

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