Research workbench
Crystal structure of murine MHC-I H-2DD in complex with murine BETA2- microglobulin and a variant of peptide (PV9) of HIV GP120 mn isolate (igpgrafyv)
Analyse Crystal structure of murine MHC-I H-2DD in complex with murine BETA2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KD7
- Type
- protein
- Length
- 1,522 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; Peptide…
- UniProt
- P01900, P01887
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | H-2 class I histocompatibility antigen, D-D alpha chain | protein | 273 | 28% helix, 39% strand | P01900 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| P, E, H, K | Peptide (PV9) of HIV GP120 mn isolate (igpgrafyv) | protein | 9 | 0% helix, 0% strand | — |
| D, G, J | Beta-2-microglobulin | protein | 100 | 0% helix, 54% strand | P01887 |
| F | H-2 class I histocompatibility antigen, D-D alpha chain | protein | 275 | 27% helix, 39% strand | P01900 |
| I | H-2 class I histocompatibility antigen, D-D alpha chain | protein | 266 | 28% helix, 39% strand | P01900 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, F, C, D, H, E, I, K
- GOL · Glycerol · additive · 2 copies · chains F, I, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.78 | 0.81 | 49 | empty |
| 2 | 446 | 0.75 | 0.84 | 47 | empty |
| 3 | 649 | 0.69 | 0.77 | 77 | EDO |
| 4 | 439 | 0.68 | 0.80 | 47 | empty |
| 5 | 591 | 0.67 | 0.77 | 54 | empty |
Interfaces
21 interfaces between chains.
- F–G · 1428 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 1379 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1224 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1220 Ų buried · 18 hydrogen bonds · protein-protein
- I–K · 899 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 covalent (disulfide, additive adduct).
Compared structures
- 5KD7 · Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a… · the same entry in another collection · chain K against K, 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 P01887
- Elsewhere: RCSB PDB 5KD7 · PDBe 5KD7 · UniProt P01900 · UniProt P01887
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