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Crystal structures of high affinity human T-cell receptors bound to pmhc reveal native diagonal binding geometry

Analyse Crystal structures of high affinity human T-cell receptors bound to pmhc reveal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P5E
Type: protein
Length: 820 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
UniProt: P01892, P61769, P78358, A2NVQ1, Q2YDB4
Ligands: MG, SO4
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-2 alpha chain	protein	276	27% helix, 40% strand	P01892
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	CANCER/TESTIS antigen 1B	protein	9	0% helix, 0% strand	P78358
D	T-cell receptor, alpha chain	protein	194	5% helix, 51% strand	A2NVQ1
E	Hypothetical protein	protein	241	7% helix, 50% strand	Q2YDB4

Ligands and binding sites

MG · Magnesium ion · metal · chains B
SO4 · Sulfate ion · ion · 5 copies · chains A, B, D, E
GOL · Glycerol · additive · 8 copies · chains A, C, D, B, E
IPA · Isopropyl alcohol · additive · chains A, C, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	781	0.73	0.79	79	empty
2	580	0.68	0.77	51	GOL, SO4
3	108	0.57	0.85	18	GOL
4	56	0.54	0.88	17	IPA
5	195	0.51	0.77	44	empty

Interfaces

7 interfaces between chains.

D–E · 2081 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1401 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 816 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 526 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 386 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2P5E · Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native… · the same entry in another collection · chain B against B, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
P78358 · AlphaFold monomer V2.0 prediction for CANCER/TESTIS antigen 1 (P78358) · a predicted model of the same protein · chain C against A, TM-score 0.27

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 P01892
Every structure of UniProt P61769
Every structure of UniProt P78358
Every structure of UniProt A2NVQ1
Every structure of UniProt Q2YDB4
Elsewhere: RCSB PDB 2P5E · PDBe 2P5E · UniProt P01892 · UniProt P61769 · UniProt P78358 · UniProt A2NVQ1 · UniProt Q2YDB4

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