MolNFT v1 · #135203 · protein

Crystal structure of MHC-I H2-kd complexed with peptides of mycobacterial tuberculosis (yqsglsivm)

5TRZ · H-2 class I histocompatibility antigen, K-D alpha chain: “Crystal structure of MHC-I H2-kd complexed with peptides of mycobacterial tuberculosis (yqsglsivm)”. X-ray diffraction, 12 pockets (best druggability 0.72). MolNFT v1 #135203…

PDB: 5TRZ
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, K-D alpha chain; Beta-2-microglobulin; Peptide…
UniProt: P01902, P61769, P9WQP1
Pockets: 12 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	H-2 class I histocompatibility antigen, K-D alpha chain	protein	275	27% helix, 41% strand	P01902
B, D	Beta-2-microglobulin	protein	100	0% helix, 51% strand	P61769
P, Q	Peptide (P9) of MTB85B (mycobacterium tuberculosis) yqsglsivm	protein	9	0% helix, 0% strand	P9WQP1

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, Q, D
GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

12 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	709	0.72	0.78	62	GOL
2	683	0.69	0.77	61	GOL
3	165	0.48	0.77	30	empty
4	166	0.46	0.76	31	empty
5	70	0.42	0.81	17	empty

Interfaces

5 interfaces between chains.

C–D · 1365 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1346 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 1014 Å² buried · 22 hydrogen bonds · protein-protein
C–Q · 961 Å² buried · 22 hydrogen bonds · protein-protein
A–P · 946 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5TRZ · Crystal structure of MHC-I H2-KD complexed with peptides of Mycobacterial tuberculosis… · the same entry in another collection · chain Q against Q, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D against A, TM-score 0.98
P01902 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.98
P9WQP1 · AlphaFold monomer V2.0 prediction for diacylglycerol ACYLTRANSFERASE/MYCOLYLTRANSFERASE… · a predicted model of the same protein · chain P against A, TM-score 0.39

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 P01902
Every structure of UniProt P61769
Every structure of UniProt P9WQP1
Elsewhere: RCSB PDB 5TRZ · PDBe 5TRZ · UniProt P01902 · UniProt P61769 · UniProt P9WQP1

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