MolNFT v1 · #98397 · protein

Crystal structure of the H2DB in complex with the np-N5D peptide

4L8D · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of the H2DB in complex with the np-N5D peptide”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.76). MolNFT v1 #98397 on GenesisL1: 3D…

PDB: 4L8D
Type: protein
Length: 768 residues
Chains: 6
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-N5D…
UniProt: P01899, P01887
Ligands: SO4
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	H-2 class I histocompatibility antigen, D-B alpha chain	protein	277	27% helix, 39% strand	P01899
B, D	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P01887
E, F	Np-N5D peptide	protein	9	0% helix, 0% strand	—

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	882	0.76	0.79	81	SO4
2	678	0.67	0.76	65	empty
3	638	0.66	0.76	60	empty
4	79	0.46	0.82	16	empty
5	80	0.46	0.82	17	empty

Interfaces

7 interfaces between chains.

C–D · 1181 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1133 Å² buried · 22 hydrogen bonds · protein-protein
A–E · 905 Å² buried · 26 hydrogen bonds · protein-protein
C–F · 830 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 311 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4L8D · Crystal structure of the H2Db in complex with the NP-N5D peptide · 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 0.99

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 4L8D · PDBe 4L8D · UniProt P01899 · UniProt P01887

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