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Crystal sturucture of L,D-transpeptidase LDTMT2 from mycobacterium tuberculosis in complex with imipenem adduct
Analyse Crystal sturucture of L,D-transpeptidase LDTMT2 from mycobacterium tuberculosis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IYW
- Type
- protein
- Length
- 1,591 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase 2
- EC
- 2.3.2.-
- UniProt
- I6Y9J2
- Ligands
- IM2
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 266 | 12% helix, 39% strand | I6Y9J2 |
| C | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 267 | 12% helix, 39% strand | I6Y9J2 |
| D, E, F | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 264 | 13% helix, 40% strand | I6Y9J2 |
Ligands and binding sites
- IM2 · (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid · ligand · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 24 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.76 | 0.78 | 107 | IM2, GOL |
| 2 | 543 | 0.69 | 0.79 | 67 | GOL |
| 3 | 405 | 0.64 | 0.78 | 46 | IM2 |
| 4 | 341 | 0.61 | 0.78 | 40 | IM2 |
| 5 | 198 | 0.60 | 0.81 | 37 | IM2 |
Interfaces
9 interfaces between chains.
- B–D · 406 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 227 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 222 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 205 Ų buried · 2 hydrogen bonds · protein-protein
- C–F · 191 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6IYW · Crystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in… · the same entry in another collection · chain F against F, TM-score 1.00
- I6Y9J2 · AlphaFold monomer V2.0 prediction for L,D-transpeptidase 2 (I6Y9J2) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 I6Y9J2
- Elsewhere: RCSB PDB 6IYW · PDBe 6IYW · UniProt I6Y9J2
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