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Crystal structure of mtb aspartate decarboxylase, 6-chlorine pyrazinoic acid complex
Analyse Crystal structure of mtb aspartate decarboxylase, 6-chlorine pyrazinoic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P02
- Type
- protein
- Length
- 1,368 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate 1-decarboxylase beta chain; Aspartate 1-decarboxylase alpha chain
- EC
- 4.1.1.11
- UniProt
- P9WIL3
- Ligands
- PYR, NMJ
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W | Aspartate 1-decarboxylase beta chain | protein | 24 | 0% helix, 67% strand | P9WIL3 |
| B, D, F, H, J, L, N, P, R, T, V, X | Aspartate 1-decarboxylase alpha chain (EC 4.1.1.11) | protein | 90 | 18% helix, 43% strand | P9WIL3 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 12 copies · chains B, D, F, H, J, L, N, P, R, T, V, X
- NMJ · 6-chloropyrazine-2-carboxylic acid · ligand · 12 copies · chains B, G, H, A, D, C, F, E, J, O, P, I, L, K, N, M, R, W, X, Q, T, S, V, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.80 | 0.82 | 81 | PYR, NMJ |
| 2 | 1003 | 0.80 | 0.81 | 66 | empty |
| 3 | 992 | 0.79 | 0.81 | 70 | empty |
| 4 | 99 | 0.75 | 0.96 | 22 | PYR, NMJ |
| 5 | 80 | 0.74 | 0.97 | 21 | PYR, NMJ |
Interfaces
68 interfaces between chains.
- S–T · 1673 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1667 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1661 Ų buried · 34 hydrogen bonds · protein-protein
- M–N · 1653 Ų buried · 39 hydrogen bonds · protein-protein
- I–J · 1646 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 6P02 · Crystal structure of Mtb aspartate decarboxylase, 6-Chlorine pyrazinoic acid complex · the same entry in another collection · chain F against F, 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 P9WIL3
- Elsewhere: RCSB PDB 6P02 · PDBe 6P02 · UniProt P9WIL3
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