Research workbench
Human constitutive 20S proteasome in complex with carfilzomib
Analyse Human constitutive 20S proteasome in complex with carfilzomib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R67
- Type
- protein
- Length
- 12,572 residues
- Chains
- 56
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha type-6; Proteasome subunit alpha type-2; Proteasome subunit…
- EC
- 3.4.25.1
- UniProt
- P60900, P25787, P25789, O14818, P28066, P25786, P25788, P28072, Q99436, P49720, P49721, P28074, P20618, P28070
- Ligands
- 3BV
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 14 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O, c, q | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 244 | 38% helix, 25% strand | P60900 |
| B, P, d, r | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 233 | 33% helix, 27% strand | P25787 |
| C, Q, e, s | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 250 | 37% helix, 27% strand | P25789 |
| D, R, f, t | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 243 | 37% helix, 23% strand | O14818 |
| E, S, g, u | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 234 | 34% helix, 28% strand | P28066 |
| F, T, h, v | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 238 | 34% helix, 26% strand | P25786 |
| G, U, i, w | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 245 | 35% helix, 27% strand | P25788 |
| H, V, j, x | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 202 | 35% helix, 31% strand | P28072 |
| I, W, k, y | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 220 | 30% helix, 32% strand | Q99436 |
| J, X, l, z | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 30% helix, 33% strand | P49720 |
| K, Y, m, 0 | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 199 | 33% helix, 35% strand | P49721 |
| L, Z, n, 3 | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 201 | 36% helix, 35% strand | P28074 |
| M, 1, o, a | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 213 | 30% helix, 33% strand | P20618 |
| N, 2, p, b | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 217 | 34% helix, 33% strand | P28070 |
Ligands and binding sites
- 3BV · N-{(2S)-2-[(morpholin-4-ylacetyl)amino]-4-phenylbutanoyl}-L-leucyl-N-[(2R,3S,4S)-1,3-dihydroxy-2,6-dimethylheptan-4-yl]-L-phenylalaninamide · ligand · 11 copies · chains H, I, J, L, M, V, W, X, Z, 1, j, k, l, n, o, y, z, 3, a
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 | 1005 | 0.80 | 0.81 | 121 | empty |
| 2 | 1003 | 0.79 | 0.81 | 91 | empty |
| 3 | 1038 | 0.79 | 0.81 | 103 | empty |
| 4 | 1179 | 0.79 | 0.81 | 136 | empty |
| 5 | 1004 | 0.79 | 0.81 | 89 | empty |
Interfaces
178 interfaces between chains.
- y–z · 1621 Ų buried · 29 hydrogen bonds · protein-protein
- k–l · 1608 Ų buried · 29 hydrogen bonds · protein-protein
- W–X · 1603 Ų buried · 26 hydrogen bonds · protein-protein
- I–J · 1602 Ų buried · 26 hydrogen bonds · protein-protein
- c–d · 1480 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 covalent (covalent ligand).
Compared structures
- 4R67 · Human constitutive 20S proteasome in complex with carfilzomib · 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 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 P28072
- Every structure of UniProt Q99436
- Every structure of UniProt P49720
- Every structure of UniProt P49721
- Every structure of UniProt P28074
- Every structure of UniProt P20618
- Every structure of UniProt P28070
- Elsewhere: RCSB PDB 4R67 · PDBe 4R67 · UniProt P60900 · UniProt P25787 · UniProt P25789 · UniProt O14818 · UniProt P28066 · UniProt P25786 · UniProt P25788 · UniProt P28072 · UniProt Q99436 · UniProt P49720 · UniProt P49721 · UniProt P28074 · UniProt P20618 · UniProt P28070
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