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Crystal structure of mouse H-2DD in complex with peptide P18-I10 derived from human immunodeficiency virus envelope glycoprotein 120

Analyse Crystal structure of mouse H-2DD in complex with peptide P18-I10 derived from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ECB
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-D alpha chain; Beta-2 microglobulin; Peptide…
UniProt: P01900, Q91XJ8, P19551
Ligands: MG
Pockets: 6 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-D alpha chain	protein	273	27% helix, 39% strand	P01900
B	Beta-2 microglobulin	protein	99	0% helix, 53% strand	Q91XJ8
P	Peptide P18-I10 from HIV GP160	protein	10	0% helix, 0% strand	P19551

Ligands and binding sites

MG · Magnesium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, P

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

Pockets

6 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	231	0.63	0.82	27	EDO
2	326	0.59	0.77	34	empty
3	187	0.53	0.78	31	EDO
4	207	0.51	0.77	27	empty
5	56	0.33	0.77	14	empty

Interfaces

2 interfaces between chains.

A–B · 1281 Å² buried · 18 hydrogen bonds · protein-protein
A–P · 916 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3ECB · Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human… · the same entry in another collection · chain A against A, TM-score 1.00
P01900 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, D-D alpha… · a predicted model of the same protein · chain A 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 P01900
Every structure of UniProt Q91XJ8
Every structure of UniProt P19551
Elsewhere: RCSB PDB 3ECB · PDBe 3ECB · UniProt P01900 · UniProt Q91XJ8 · UniProt P19551

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