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Crystal structure of the 5CC7 TCR in complex with 5C2/I-ek

Analyse Crystal structure of the 5CC7 TCR in complex with 5C2/I-ek in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4P2Q
Type: protein
Length: 3,215 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class II histocompatibility antigen, E-K alpha chain; MHC class II E-beta-K; 5C2…
UniProt: P04224, Q31163
Ligands: NAG
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 8 distinct chains · 12% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, K	H-2 class II histocompatibility antigen, E-K alpha chain	protein	180	14% helix, 47% strand	P04224
B, G, L, Q	MHC class II E-beta-K	protein	171	19% helix, 44% strand	Q31163
C, H	5C2 peptide	protein	14	0% helix, 14% strand	—
D, I, N, S	5CC7 T-cell receptor alpha chain	protein	196	7% helix, 51% strand	—
E, J	5CC7 T-cell receptor beta chain	protein	245	9% helix, 49% strand	—
M, R	5C2 peptide	protein	13	0% helix, 15% strand	—
O, T	5CC7 T-cell receptor beta chain	protein	242	10% helix, 50% strand	—
P	H-2 class II histocompatibility antigen, E-K alpha chain	protein	179	15% helix, 47% strand	P04224

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, G, K, L

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	927	0.79	0.82	103	empty
2	998	0.78	0.80	99	empty
3	534	0.72	0.81	72	empty
4	529	0.72	0.81	61	empty
5	442	0.71	0.82	46	empty

Interfaces

54 interfaces between chains.

F–G · 2626 Å² buried · 39 hydrogen bonds · protein-protein
P–Q · 2585 Å² buried · 36 hydrogen bonds · protein-protein
K–L · 2574 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 2570 Å² buried · 39 hydrogen bonds · protein-protein
N–O · 2189 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

4P2Q · Crystal structure of the 5cc7 TCR in complex with 5c2/I-Ek · the same entry in another collection · chain T against T, TM-score 1.00

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 P04224
Every structure of UniProt Q31163
Elsewhere: RCSB PDB 4P2Q · PDBe 4P2Q · UniProt P04224 · UniProt Q31163

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