MolNFT v1 · #13503 · protein

Crystal structure of murine MHC class I H-2LD with a mixture of bound peptides

1LDP: “Crystal structure of murine MHC class I H-2LD with a mixture of bound peptides”. X-ray diffraction, 2 ligands (NAG, NDG), 3 pockets (best druggability 0.64). MolNFT v1 #13503 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1LDP
Type: protein
Length: 389 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I H-2LD; Peptide
UniProt: P01897, P01887
Ligands: NAG, NDG
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	MHC class I H-2LD	protein	272	26% helix, 32% strand	P01897
L	MHC class I H-2LD	protein	99	0% helix, 39% strand	P01887
P	Peptide	protein	9	0% helix, 78% strand	—
Q	Peptide	protein	9	0% helix, 78% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H
NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains H

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	534	0.64	0.76	53	empty
2	136	0.53	0.81	27	empty
3	79	0.38	0.78	16	empty

Interfaces

4 interfaces between chains.

H–L · 1257 Å² buried · 13 hydrogen bonds · protein-protein
H–Q · 937 Å² buried · 19 hydrogen bonds · protein-protein
H–P · 733 Å² buried · 16 hydrogen bonds · protein-protein
P–Q · 551 Å² buried · 58 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

1LDP · Crystal structure of murine MHC class I H-2LD with a mixture of bound peptides · the same entry in another collection · chain H against H, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain L against A, TM-score 0.97
P01897 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, L-D alpha… · a predicted model of the same protein · chain H against A, TM-score 0.96

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 P01897
Every structure of UniProt P01887
Elsewhere: RCSB PDB 1LDP · PDBe 1LDP · UniProt P01897 · UniProt P01887

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.