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Crystal structure of H2DB-NPM6W

Analyse Crystal structure of H2DB-NPM6W in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HUV
Type: protein
Length: 765 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; NPM6W…
UniProt: P01899, P01887
Ligands: SO4
Pockets: 8 · best druggability 0.77

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	H-2 class I histocompatibility antigen, D-B alpha chain	protein	275	25% helix, 37% strand	P01899
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P01887
C, F	NPM6W variant peptide	protein	9	0% helix, 0% strand	—
E	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B, D

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

Pockets

8 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	937	0.77	0.79	101	SO4
2	704	0.68	0.76	63	empty
3	651	0.66	0.75	55	empty
4	96	0.44	0.79	17	empty
5	82	0.41	0.78	14	empty

Interfaces

7 interfaces between chains.

D–E · 1177 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1163 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 936 Å² buried · 24 hydrogen bonds · protein-protein
D–F · 934 Å² buried · 25 hydrogen bonds · protein-protein
A–E · 320 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4HUV · Crystal Structure of H2Db-NPM6W · 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 E 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 4HUV · PDBe 4HUV · UniProt P01899 · UniProt P01887

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