MolNFT v1 · #138303 · protein
Crystal structure of tapbpr and H2-dd complex
5WER · H-2 class I histocompatibility antigen, D-D alpha chain: “Crystal structure of tapbpr and H2-dd complex”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #138303 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5WER
- Type
- protein
- Length
- 2,706 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-D alpha chain; Beta-2-microglobulin; Tap…
- UniProt
- P01900, P61769
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-D alpha chain | protein | 265 | 26% helix, 31% strand | P01900 |
| B, E, H, K | Beta-2-microglobulin | protein | 98 | 0% helix, 46% strand | P61769 |
| C | Tap binding protein related | protein | 317 | 1% helix, 46% strand | — |
| D | H-2 class I histocompatibility antigen, D-D alpha chain | protein | 265 | 28% helix, 35% strand | P01900 |
| F | Tap binding protein related | protein | 315 | 1% helix, 38% strand | — |
| G | H-2 class I histocompatibility antigen, D-D alpha chain | protein | 269 | 25% helix, 33% strand | P01900 |
| I | Tap binding protein related | protein | 301 | 1% helix, 34% strand | — |
| J | H-2 class I histocompatibility antigen, D-D alpha chain | protein | 270 | 22% helix, 30% strand | P01900 |
| L | Tap binding protein related | protein | 312 | 1% helix, 40% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains C, F, G, I, L
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, E
- 1PE · Pentaethylene glycol · additive · chains J
- CIT · Citric acid · additive · chains I, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.83 | 0.88 | 85 | empty |
| 2 | 976 | 0.80 | 0.82 | 103 | empty |
| 3 | 788 | 0.77 | 0.81 | 81 | empty |
| 4 | 557 | 0.77 | 0.84 | 70 | empty |
| 5 | 681 | 0.77 | 0.82 | 68 | empty |
Interfaces
26 interfaces between chains.
- A–C · 1487 Ų buried · 24 hydrogen bonds · protein-protein
- J–L · 1359 Ų buried · 28 hydrogen bonds · protein-protein
- G–I · 1332 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1274 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1264 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 2 covalent (disulfide, additive adduct).
Compared structures
- 5WER · Crystal Structure of TAPBPR and H2-Dd complex · the same entry in another collection · chain L against L, 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 P01900
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5WER · PDBe 5WER · UniProt P01900 · UniProt P61769
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