Research workbench
Crystal structure of murine MHC-I H-2DD in complex with murine BETA2- microglobulin and a variant of peptide (PVI10) of HIV GP120 mn isolate (igpgrafyvi)
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
- 5KD4
- Type
- protein
- Length
- 764 residues
- Chains
- 6
- 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 of…
- UniProt
- P01900, P01887
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 18% 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 | 25% helix, 39% strand | P01900 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 51% strand | P01887 |
| P, Q | Peptide of HIV GP120 mn isolate, PVI10 (igpgrafyvi) | protein | 10 | 0% helix, 0% strand | — |
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.79 | 0.81 | 116 | empty |
| 2 | 292 | 0.63 | 0.80 | 24 | empty |
| 3 | 292 | 0.61 | 0.79 | 42 | empty |
| 4 | 94 | 0.60 | 0.88 | 22 | empty |
| 5 | 131 | 0.58 | 0.83 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1359 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1295 Ų buried · 11 hydrogen bonds · protein-protein
- C–Q · 900 Ų buried · 14 hydrogen bonds · protein-protein
- A–P · 882 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5KD4 · Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a… · the same entry in another collection · chain Q against Q, TM-score 1.00
- P01900 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, D-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 5KD4 · PDBe 5KD4 · UniProt P01900 · UniProt P01887
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