MolNFT v1 · #173474 · protein
Human immunoproteasome 20S particle in complex with [2-(3- ethylphenyl)-1-[(2S)-3-phenyl-2-[(pyrazin-2-yl) FORMAMIDO]PROPANAMIDO]ETHYL]BORONIC acid
7B12 · Proteasome subunit beta type-1: “Human immunoproteasome 20S particle in complex with [2-(3- ethylphenyl)-1-[(2S)-3-phenyl-2-[(pyrazin-2-yl)…”. X-ray diffraction, 3 ligands (SKN, NA, SO4), 20 pockets (best druggability 0.80). MolNFT…
- PDB
- 7B12
- Type
- protein
- Length
- 6,195 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit beta type-1; Proteasome subunit beta type-4; Proteasome subunit alpha…
- EC
- 3.4.25.1
- UniProt
- P20618, P28070, P60900, P25787, P25789, O14818, P28066, P25786, P25788, P28065, P49720, P49721, P28062, P40306
- Ligands
- SKN, NA, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 21 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, M | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 213 | 31% helix, 33% strand | P20618 |
| 2, N | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 214 | 35% helix, 34% strand | P28070 |
| A | Proteasome subunit alpha type-6 | protein | 240 | 40% helix, 25% strand | P60900 |
| B, P | Proteasome subunit alpha type-2 | protein | 229 | 36% helix, 27% strand | P25787 |
| C | Proteasome subunit alpha type-4 | protein | 241 | 39% helix, 26% strand | P25789 |
| D | Proteasome subunit alpha type-7 | protein | 227 | 41% helix, 26% strand | O14818 |
| E | Proteasome subunit alpha type-5 | protein | 230 | 35% helix, 28% strand | P28066 |
| F, T | Proteasome subunit alpha type-1 | protein | 236 | 35% helix, 26% strand | P25786 |
| G | Proteasome subunit alpha type-3 | protein | 242 | 38% helix, 27% strand | P25788 |
| H, V | Proteasome subunit beta type-9 (EC 3.4.25.1) | protein | 199 | 35% helix, 33% strand | P28065 |
| J, X | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 30% helix, 32% strand | P49720 |
| K | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 196 | 33% helix, 37% strand | P49721 |
| L, Z | Proteasome subunit beta type-8 (EC 3.4.25.1) | protein | 203 | 36% helix, 35% strand | P28062 |
| O | Proteasome subunit alpha type-6 | protein | 240 | 40% helix, 25% strand | P60900 |
| Q | Proteasome subunit alpha type-4 | protein | 245 | 39% helix, 26% strand | P25789 |
| U | Proteasome subunit alpha type-3 | protein | 243 | 37% helix, 27% strand | P25788 |
| Y | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 197 | 33% helix, 37% strand | P49721 |
| i | Proteasome subunit beta type-10 (EC 3.4.25.1) | protein | 219 | 30% helix, 35% strand | P40306 |
| r | Proteasome subunit alpha type-7 | protein | 229 | 38% helix, 25% strand | O14818 |
| s | Proteasome subunit alpha type-5 | protein | 230 | 33% helix, 27% strand | P28066 |
| w | Proteasome subunit beta type-10 (EC 3.4.25.1) | protein | 220 | 30% helix, 35% strand | P40306 |
Ligands and binding sites
- SKN · ((R)-2-(3-ethylphenyl)-1-((S)-3-phenyl-2-(pyrazine-2-carboxamido)propanamido)ethyl)boronic acid · ligand · 6 copies · chains H, i, L, M, V, w, 1, Z, J, X
- NA · Sodium ion · metal · 6 copies · chains A, L, X, O, J, Z, 1, i, M, w
- SO4 · Sulfate ion · ion · 5 copies · chains 1, Z, D, K, L, M, Y, r
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 | 800 | 0.80 | 0.83 | 86 | empty |
| 2 | 696 | 0.79 | 0.83 | 74 | empty |
| 3 | 537 | 0.78 | 0.85 | 69 | empty |
| 4 | 700 | 0.78 | 0.83 | 77 | empty |
| 5 | 1195 | 0.78 | 0.80 | 115 | empty |
Interfaces
86 interfaces between chains.
- X–w · 1603 Ų buried · 24 hydrogen bonds · protein-protein
- J–i · 1577 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1529 Ų buried · 19 hydrogen bonds · protein-protein
- P–Q · 1524 Ų buried · 20 hydrogen bonds · protein-protein
- Q–r · 1498 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7B12 · HUMAN IMMUNOPROTEASOME 20S PARTICLE IN COMPLEX WITH… · the same entry in another collection · chain J against J, 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 P20618
- Every structure of UniProt P28070
- Every structure of UniProt P60900
- Every structure of UniProt P25787
- Every structure of UniProt P25789
- Every structure of UniProt O14818
- Every structure of UniProt P28066
- Every structure of UniProt P25786
- Every structure of UniProt P25788
- Every structure of UniProt P28065
- Every structure of UniProt P49720
- Every structure of UniProt P49721
- Every structure of UniProt P28062
- Every structure of UniProt P40306
- Elsewhere: RCSB PDB 7B12 · PDBe 7B12 · UniProt P20618 · UniProt P28070 · UniProt P60900 · UniProt P25787 · UniProt P25789 · UniProt O14818 · UniProt P28066 · UniProt P25786 · UniProt P25788 · UniProt P28065 · UniProt P49720 · UniProt P49721 · UniProt P28062 · UniProt P40306
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