MolNFT v1 · #178538 · protein
Cryo-EM structure of a membrane PROTEIN(LL)
7FJE · T-cell surface glycoprotein CD3 zeta chain: “Cryo-EM structure of a membrane PROTEIN(LL)”. Electron microscopy, 1 ligand (CLR), 14 pockets (best druggability 0.84). MolNFT v1 #178538 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7FJE
- Type
- protein
- Length
- 1,058 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD3 zeta chain; T-cell surface glycoprotein CD3 delta chain…
- UniProt
- P20963, P04234, P07766, P09693, A0A0B4J271, A0N4Z6, P01848, A0A0K0K1A5, P0DSE2, A0A0G2JMB4
- Ligands
- CLR
- Pockets
- 14 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | T-cell surface glycoprotein CD3 zeta chain | protein | 33 | 76% helix, 0% strand | P20963 |
| b | T-cell surface glycoprotein CD3 zeta chain | protein | 29 | 72% helix, 0% strand | P20963 |
| d | T-cell surface glycoprotein CD3 delta chain | protein | 107 | 21% helix, 36% strand | P04234 |
| e | T-cell surface glycoprotein CD3 epsilon chain | protein | 123 | 24% helix, 29% strand | P07766 |
| f | T-cell surface glycoprotein CD3 epsilon chain | protein | 120 | 23% helix, 32% strand | P07766 |
| g | T-cell surface glycoprotein CD3 gamma chain | protein | 113 | 26% helix, 38% strand | P09693 |
| m | T cell receptor alpha variable 12-3,POSSIBLE J 11 gene SEGMENT,T cell receptor alpha chain constant | protein | 246 | 16% helix, 33% strand | A0A0B4J271, A0N4Z6, P01848 |
| n | T cell receptor beta variable 6-5,M1-specific T cell receptor beta CHAIN,T cell receptor beta constant 2 | protein | 287 | 17% helix, 39% strand | A0A0K0K1A5, P0DSE2, A0A0G2JMB4 |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains b, g, n
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.84 | 0.85 | 108 | empty |
| 2 | 970 | 0.80 | 0.81 | 67 | CLR |
| 3 | 1014 | 0.76 | 0.78 | 54 | empty |
| 4 | 1020 | 0.71 | 0.75 | 91 | empty |
| 5 | 56 | 0.67 | 0.95 | 22 | empty |
Interfaces
22 interfaces between chains.
- m–n · 3756 Ų buried · 19 hydrogen bonds · protein-protein
- d–e · 1632 Ų buried · 16 hydrogen bonds · protein-protein
- f–g · 1626 Ų buried · 18 hydrogen bonds · protein-protein
- d–m · 1117 Ų buried · 10 hydrogen bonds · protein-protein
- a–b · 745 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 7FJE · Cryo-EM structure of a membrane protein(LL) · the same entry in another collection · chain m against m, TM-score 1.00
- P0DSE2 · AlphaFold monomer V2.0 prediction for M1-specific T cell receptor beta chain (P0DSE2) · a predicted model of the same protein · chain n against A, TM-score 0.93
- P07766 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD3 epsilon chain… · a predicted model of the same protein · chain f against A, TM-score 0.85
- P04234 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD3 delta chain (P04234) · a predicted model of the same protein · chain d against A, TM-score 0.66
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 P20963
- Every structure of UniProt P04234
- Every structure of UniProt P07766
- Every structure of UniProt P09693
- Every structure of UniProt A0A0B4J271
- Every structure of UniProt A0N4Z6
- Every structure of UniProt P01848
- Every structure of UniProt A0A0K0K1A5
- Every structure of UniProt P0DSE2
- Every structure of UniProt A0A0G2JMB4
- Elsewhere: RCSB PDB 7FJE · PDBe 7FJE · UniProt P20963 · UniProt P04234 · UniProt P07766 · UniProt P09693 · UniProt A0A0B4J271 · UniProt A0N4Z6 · UniProt P01848 · UniProt A0A0K0K1A5 · UniProt P0DSE2 · UniProt A0A0G2JMB4
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