MolNFT v1 · #103921 · protein

Crystal structure of H2KB-Q600V complex

4PV9 · H-2 class I histocompatibility antigen, K-B alpha chain: “Crystal structure of H2KB-Q600V complex”. X-ray diffraction, 12 pockets (best druggability 0.66). MolNFT v1 #103921 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4PV9
Type: protein
Length: 769 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; S598…
UniProt: P01901, P01887
Pockets: 12 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 23% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, K-B alpha chain	protein	278	27% helix, 39% strand	P01901
B, D	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
C	H-2 class I histocompatibility antigen, K-B alpha chain	protein	277	28% helix, 39% strand	P01901
E, F	S598 peptide modified Q600V	protein	8	0% helix, 0% strand	—

Ligands and binding sites

ACT · Acetate ion · additive · 2 copies · chains C, D
GOL · Glycerol · additive · chains C, D

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	746	0.66	0.75	64	empty
2	753	0.66	0.74	63	GOL
3	132	0.51	0.80	19	empty
4	189	0.50	0.77	35	empty
5	133	0.48	0.78	22	empty

Interfaces

5 interfaces between chains.

C–D · 1221 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1209 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 880 Å² buried · 23 hydrogen bonds · protein-protein
C–F · 877 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 731 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 modified (disulfide, nonstandard).

Compared structures

4PV9 · Crystal Structure of H2Kb-Q600V complex · 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 P01901
Every structure of UniProt P01887
Elsewhere: RCSB PDB 4PV9 · PDBe 4PV9 · UniProt P01901 · UniProt P01887

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