MolNFT v1 · #162223 · protein
NYBR1-A2-slskildtv
6R2L · HLA class I histocompatibility antigen, a-2 alpha chain: “NYBR1-A2-slskildtv”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.76). MolNFT v1 #162223 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6R2L
- Type
- protein
- Length
- 826 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, A0A0B4J277, K7N5M3, A0A584, K7N5M4
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 26% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Ser-leu-ser-lys-ile-leu-asp-thr-val | protein | 9 | 0% helix, 0% strand | — |
| D | T cell receptor alpha variable 22,HUMAN nkt TCR alpha chain | protein | 194 | 2% helix, 46% strand | A0A0B4J277, K7N5M3 |
| E | T cell receptor beta variable 11-2,HUMAN nkt TCR beta chain | protein | 247 | 7% helix, 48% strand | A0A584, K7N5M4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, D, E
- GOL · Glycerol · additive · 3 copies · chains A, E
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.76 | 0.79 | 81 | SO4 |
| 2 | 613 | 0.70 | 0.78 | 59 | SO4 |
| 3 | 150 | 0.53 | 0.80 | 20 | EDO |
| 4 | 147 | 0.48 | 0.78 | 22 | SO4 |
| 5 | 52 | 0.41 | 0.82 | 15 | SO4 |
Interfaces
7 interfaces between chains.
- D–E · 2242 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1400 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 862 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 820 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 410 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6R2L · NYBR1-A2-slskildtv · 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
- A0A584 · AlphaFold monomer V2.0 prediction for T cell receptor beta variable 11-2 (A0A584) · a predicted model of the same protein · chain E against A, TM-score 0.36
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 A0A0B4J277
- Every structure of UniProt K7N5M3
- Every structure of UniProt A0A584
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 6R2L · PDBe 6R2L · UniProt P01892 · UniProt P61769 · UniProt A0A0B4J277 · UniProt K7N5M3 · UniProt A0A584 · UniProt K7N5M4
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