MolNFT v1 · #135205 · protein
Crystal structure of MHC-I H2-kd complexed with peptides of mycobacterial tuberculosis (yyqsglsiv)
5TS1 · H-2 class I histocompatibility antigen, K-D alpha chain: “Crystal structure of MHC-I H2-kd complexed with peptides of mycobacterial tuberculosis (yyqsglsiv)”. X-ray diffraction, 18 pockets (best druggability 0.71). MolNFT v1 #135205…
- PDB
- 5TS1
- Type
- protein
- Length
- 1,528 residues
- Chains
- 12
- 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
- 18 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | H-2 class I histocompatibility antigen, K-D alpha chain | protein | 273 | 27% helix, 39% strand | P01902 |
| B, D, F, H | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| P, Q, R, S | Peptide (P9) of MTB85B (mycobacterium tuberculosis) yyqsglsiv | protein | 9 | 0% helix, 0% strand | P9WQP1 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.71 | 0.77 | 57 | GOL |
| 2 | 739 | 0.71 | 0.77 | 62 | GOL |
| 3 | 736 | 0.70 | 0.77 | 72 | EDO |
| 4 | 732 | 0.70 | 0.77 | 60 | GOL |
| 5 | 475 | 0.60 | 0.75 | 50 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1430 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1421 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1383 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1360 Ų buried · 17 hydrogen bonds · protein-protein
- A–P · 992 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5TS1 · Crystal structure of MHC-I H2-KD complexed with peptides of Mycobacterial tuberculosis… · the same entry in another collection · chain S against S, 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 P01902
- Every structure of UniProt P61769
- Every structure of UniProt P9WQP1
- Elsewhere: RCSB PDB 5TS1 · PDBe 5TS1 · UniProt P01902 · UniProt P61769 · UniProt P9WQP1
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