MolNFT v1 · #127537 · protein

Structure of H-2DB in complex with teipp apl TRH4 P3P

5MZM · H-2 class I histocompatibility antigen, D-B alpha chain: “Structure of H-2DB in complex with teipp apl TRH4 P3P”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.68). MolNFT v1 #127537 on GenesisL1: 3D structure…

PDB: 5MZM
Type: protein
Length: 758 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; Ceramide…
UniProt: P01899, P01887
Ligands: SO4
Pockets: 10 · best druggability 0.68

Structure

x-ray diffraction · 4 distinct chains · 20% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	271	25% helix, 40% strand	P01899
B, E	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
C, F	Ceramide synthase 5 derived peptide TRH4 P3P	protein	9	0% helix, 0% strand	—
D	H-2 class I histocompatibility antigen, D-B alpha chain	protein	271	24% helix, 39% strand	P01899

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B
GOL · Glycerol · additive · chains A

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	726	0.68	0.76	60	empty
2	637	0.64	0.74	64	empty
3	83	0.41	0.79	22	empty
4	79	0.40	0.79	22	empty
5	96	0.39	0.76	20	empty

Interfaces

5 interfaces between chains.

A–B · 1356 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1278 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 892 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 890 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 732 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5MZM · Structure of H-2Db in complex with TEIPP APL Trh4 p3P · 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 0.98

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 5MZM · PDBe 5MZM · UniProt P01899 · UniProt P01887

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