Research workbench

Crystal structure of the H2DB in complex with the np-N3D peptide

Analyse Crystal structure of the H2DB in complex with the np-N3D peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4L8C
Type: protein
Length: 1,525 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; Np-N3D…
UniProt: P01899, P01887
Ligands: SO4
Pockets: 19 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	H-2 class I histocompatibility antigen, D-B alpha chain	protein	275	26% helix, 38% strand	P01899
B, D, H	Beta-2-microglobulin	protein	97	0% helix, 51% strand	P01887
F	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P01887
I, J, K, L	Np-N3D peptide	protein	9	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, G, D, E, F

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

Pockets

19 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	1122	0.74	0.77	79	SO4
2	951	0.70	0.75	86	empty
3	821	0.69	0.75	64	empty
4	700	0.68	0.76	67	empty
5	608	0.66	0.76	49	empty

Interfaces

17 interfaces between chains.

E–F · 1173 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 1172 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1168 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1143 Å² buried · 20 hydrogen bonds · protein-protein
A–I · 934 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4L8C · Crystal structure of the H2Db in complex with the NP-N3D peptide · 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
Elsewhere: RCSB PDB 4L8C · PDBe 4L8C · UniProt P01899 · UniProt P01887

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