MolNFT v1 · #107122 · protein
Crystal structure of M. tuberculosis CLPP1P2 bound to adep and agonist
4U0G · ATP-dependent clp protease proteolytic subunit 2: “Crystal structure of M. tuberculosis CLPP1P2 bound to adep and agonist”. X-ray diffraction, 4 ligands (ZIL, 39Y, 3A0), 20 pockets (best druggability 0.74). MolNFT v1 #107122 on…
- PDB
- 4U0G
- Type
- protein
- Length
- 5,250 residues
- Chains
- 42
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit 2; ATP-dependent clp protease proteolytic…
- EC
- 3.4.21.92
- UniProt
- P9WPC3, P9WPC5
- Ligands
- ZIL, 39Y, 3A0, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 12 distinct chains · 46% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 197 | 43% helix, 28% strand | P9WPC3 |
| B | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 197 | 43% helix, 27% strand | P9WPC3 |
| C, F, G, O, R, S, T, U | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 196 | 43% helix, 28% strand | P9WPC3 |
| D, Q | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 195 | 44% helix, 28% strand | P9WPC3 |
| H | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 174 | 49% helix, 24% strand | P9WPC5 |
| I, K | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 172 | 49% helix, 24% strand | P9WPC5 |
| J, V, W, X | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 175 | 48% helix, 24% strand | P9WPC5 |
| L, N, Y, a | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 174 | 48% helix, 24% strand | P9WPC5 |
| M | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 173 | 49% helix, 24% strand | P9WPC5 |
| P | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 194 | 44% helix, 28% strand | P9WPC3 |
| Z, b | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 175 | 49% helix, 24% strand | P9WPC5 |
| c, i, d, e, f, g, h, j, k, l, m, n, o, p | Adep-2B5ME | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZIL · N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine · ligand · 28 copies · chains A, B, C, D, E, F, G, H, N, I, J, K, L, M, O, P, Q, R, S, T, U, V, b, W, X, Y, Z, a
- 39Y · (2E,5S)-5-methylhept-2-enoic acid · ligand · 14 copies · chains A, B, c, G, i, C, d, D, e, E, f, F, g, h, O, P, j, Q, k, R, l, S, m, T, n, U, o, p
- 3A0 · (2S,4S)-4-methylpiperidine-2-carboxylic acid · ligand · 14 copies · chains B, c, A, i, C, d, D, e, E, f, F, g, G, h, P, j, Q, k, R, l, S, m, T, n, U, o, O, p
- SO4 · Sulfate ion · ion · 35 copies · chains A, B, c, C, d, D, E, F, g, G, I, J, M, O, U, p, P, Q, R, l, S, m, T, W
- DMS · Dimethyl sulfoxide · additive · 15 copies · chains A, B, C, D, E, F, G, O, P, Q, R, S, T, U
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 | 899 | 0.74 | 0.78 | 100 | ZIL |
| 2 | 853 | 0.73 | 0.78 | 100 | ZIL |
| 3 | 904 | 0.73 | 0.77 | 104 | ZIL |
| 4 | 929 | 0.73 | 0.77 | 101 | ZIL |
| 5 | 862 | 0.73 | 0.77 | 102 | ZIL |
Interfaces
109 interfaces between chains.
- A–B · 1762 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1760 Ų buried · 23 hydrogen bonds · protein-protein
- A–G · 1740 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1734 Ų buried · 20 hydrogen bonds · protein-protein
- R–S · 1721 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 112 modified, 56 covalent (engineered, covalent ligand, additive adduct, nonstandard).
Compared structures
- 4U0G · Crystal Structure of M. tuberculosis ClpP1P2 bound to ADEP and agonist · the same entry in another collection · chain K against K, 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 P9WPC3
- Every structure of UniProt P9WPC5
- Elsewhere: RCSB PDB 4U0G · PDBe 4U0G · UniProt P9WPC3 · UniProt P9WPC5
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