Research workbench
Structure of clpp from escherichia COLI in complex with ADEP1
Analyse Structure of clpp from escherichia COLI in complex with ADEP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MT6
- Type
- protein
- Length
- 5,400 residues
- Chains
- 56
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; Acyldepsipeptide 1
- EC
- 3.4.21.92
- UniProt
- P0A6G7
- Ligands
- OTT
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 18 distinct chains · 45% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 26% strand | P0A6G7 |
| S | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 46% helix, 27% strand | P0A6G7 |
| T, U | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 46% helix, 28% strand | P0A6G7 |
| O | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 189 | 44% helix, 28% strand | P0A6G7 |
| P, X, M, J, I, F, G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 190 | 44% helix, 29% strand | P0A6G7 |
| Q | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 45% helix, 29% strand | P0A6G7 |
| Y | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 27% strand | P0A6G7 |
| Z | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 26% strand | P0A6G7 |
| a | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 28% strand | P0A6G7 |
| b | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 46% helix, 26% strand | P0A6G7 |
| V | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 27% strand | P0A6G7 |
| W | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 26% strand | P0A6G7 |
| L, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 45% helix, 28% strand | P0A6G7 |
| K, E, D, C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 188 | 45% helix, 29% strand | P0A6G7 |
| H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 27% strand | P0A6G7 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 188 | 45% helix, 28% strand | P0A6G7 |
| A | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 44% helix, 29% strand | P0A6G7 |
| 1, 2, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, v, w, x, y, z, 3, 4, u | Acyldepsipeptide 1 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- OTT · (2E,4E,6E)-octa-2,4,6-trienoic acid · ligand · 28 copies · chains A, G, 1, B, 2, C, c, D, d, E, e, F, f, g, I, H, h, J, i, K, j, L, k, M, l, N, m, n, U, O, o, P, p, Q, q, R, r, S, s, T, t, V, W, v, X, w, Y, x, Z, y, a, z, b, 3, 4, u
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 55 copies · chains R, Q, S, T, U, O, P, Y, Z, a, b, V, W, X, M, N, L, K, J, I, H, F, E, D, C, B, A, G
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 | 747 | 0.80 | 0.84 | 103 | MPD |
| 2 | 928 | 0.79 | 0.81 | 116 | MPD |
| 3 | 599 | 0.78 | 0.84 | 83 | MPD |
| 4 | 604 | 0.78 | 0.84 | 82 | MPD |
| 5 | 623 | 0.78 | 0.83 | 90 | MPD |
Interfaces
133 interfaces between chains.
- A–G · 1731 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 1648 Ų buried · 23 hydrogen bonds · protein-protein
- B–A · 1616 Ų buried · 19 hydrogen bonds · protein-protein
- D–C · 1591 Ų buried · 18 hydrogen bonds · protein-protein
- M–L · 1585 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified, 28 covalent (nonstandard, covalent ligand).
Compared structures
- 3MT6 · Structure of ClpP from Escherichia coli in complex with ADEP1 · 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 P0A6G7
- Elsewhere: RCSB PDB 3MT6 · PDBe 3MT6 · UniProt P0A6G7
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