Research workbench
Crystal structure of mycobacterium tuberculosis proteasome open-gate mutant modified by inhibitor GL1
Analyse Crystal structure of mycobacterium tuberculosis proteasome open-gate mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HF9
- Type
- protein
- Length
- 11,935 residues
- Chains
- 56
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome (alpha subunit) prca; Proteasome (beta subunit) prcb
- EC
- 3.4.25.1
- UniProt
- O33244, O33245
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 12 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K, O, Q, S, U, 1, a, b, d, f, i, k, o, q, s, u, w, y | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 211 | 38% helix, 25% strand | O33244 |
| D, Y, 3 | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 210 | 40% helix, 24% strand | O33244 |
| F | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 193 | 35% helix, 26% strand | O33244 |
| I | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 212 | 41% helix, 23% strand | O33244 |
| M | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 205 | 38% helix, 26% strand | O33244 |
| W | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 193 | 36% helix, 27% strand | O33244 |
| m | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 208 | 38% helix, 26% strand | O33244 |
| H, C, E, G, J, L, N, P, R, T, X, Z, 2, e, g, j, l, n, p, r, t, x, z, 4 | Proteasome (beta subunit) prcb (EC 3.4.25.1) | protein | 217 | 40% helix, 29% strand | O33245 |
| V | Proteasome (beta subunit) prcb (EC 3.4.25.1) | protein | 218 | 41% helix, 27% strand | O33245 |
| h | Proteasome (beta subunit) prcb (EC 3.4.25.1) | protein | 214 | 40% helix, 29% strand | O33245 |
| c | Proteasome (beta subunit) prcb (EC 3.4.25.1) | protein | 215 | 40% helix, 28% strand | O33245 |
| v | Proteasome (beta subunit) prcb (EC 3.4.25.1) | protein | 219 | 40% helix, 28% strand | O33245 |
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 | 1101 | 0.86 | 0.87 | 118 | empty |
| 2 | 608 | 0.83 | 0.88 | 48 | empty |
| 3 | 598 | 0.83 | 0.88 | 50 | empty |
| 4 | 578 | 0.83 | 0.88 | 48 | empty |
| 5 | 1155 | 0.83 | 0.84 | 103 | empty |
Interfaces
149 interfaces between chains.
- k–m · 850 Ų buried · 13 hydrogen bonds · protein-protein
- D–K · 849 Ų buried · 11 hydrogen bonds · protein-protein
- U–1 · 848 Ų buried · 13 hydrogen bonds · protein-protein
- i–s · 847 Ų buried · 12 hydrogen bonds · protein-protein
- Q–Y · 842 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (nonstandard).
Compared structures
- 3HF9 · Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant modified by… · the same entry in another collection · chain b against b, 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 O33244
- Every structure of UniProt O33245
- Elsewhere: RCSB PDB 3HF9 · PDBe 3HF9 · UniProt O33244 · UniProt O33245
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