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Crystal structure of the H2DB in complex with the np-N5H peptide

Analyse Crystal structure of the H2DB in complex with the np-N5H peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4L8B
Type: protein
Length: 383 residues
Chains: 3
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-N5H…
UniProt: P01899, P01887
Ligands: NA, SO4
Pockets: 5 · best druggability 0.60

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	276	26% helix, 39% strand	P01899
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P01887
C	Np-N5H peptide	protein	9	0% helix, 0% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains B
SO4 · Sulfate ion · ion · 2 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	509	0.60	0.74	41	NA
2	121	0.44	0.77	18	empty
3	56	0.43	0.83	18	empty
4	101	0.38	0.76	16	SO4, PEG
5	62	0.27	0.73	14	empty

Interfaces

2 interfaces between chains.

A–B · 1180 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 888 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4L8B · Crystal structure of the H2Db in complex with the NP-N5H peptide · the same entry in another collection · chain A against A, 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 0.98

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 4L8B · PDBe 4L8B · UniProt P01899 · UniProt P01887

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