MolNFT v1 · #157936 · protein
Crystal structure of RT1.AA-BU31-10
6NF7 · RT1A.A: “Crystal structure of RT1.AA-BU31-10”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #157936 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NF7
- Type
- protein
- Length
- 1,922 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RT1A.A; Beta-2-microglobulin; BU31-10 peptide
- UniProt
- P07151
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M | RT1A.A | protein | 275 | 27% helix, 37% strand | — |
| B, K, N | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P07151 |
| C | BU31-10 peptide | protein | 12 | 0% helix, 0% strand | — |
| E, H | Beta-2-microglobulin | protein | 100 | 0% helix, 48% strand | P07151 |
| F | BU31-10 peptide | protein | 10 | 0% helix, 0% strand | — |
| I | BU31-10 peptide | protein | 10 | 0% helix, 0% strand | — |
| L, O | BU31-10 peptide | protein | 9 | 0% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.81 | 0.82 | 118 | empty |
| 2 | 923 | 0.76 | 0.79 | 81 | empty |
| 3 | 518 | 0.70 | 0.80 | 44 | empty |
| 4 | 609 | 0.69 | 0.78 | 49 | empty |
| 5 | 649 | 0.69 | 0.77 | 66 | empty |
Interfaces
29 interfaces between chains.
- D–E · 1429 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1389 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 1388 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1368 Ų buried · 22 hydrogen bonds · protein-protein
- M–N · 1209 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 6NF7 · Crystal Structure of RT1.Aa-Bu31-10 · the same entry in another collection · chain O against O, 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 P07151
- Elsewhere: RCSB PDB 6NF7 · PDBe 6NF7 · UniProt P07151
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