Research workbench
Crystal structure of indole 3-carboxylic acid decarboxylase from arthrobacter nicotianae FI1612 in complex with co-factor prfmn.
Analyse Crystal structure of indole 3-carboxylic acid decarboxylase from arthrobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P9Q
- Type
- protein
- Length
- 2,714 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anind
- Ligands
- 4LU, NA, MN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anind | protein | 454 | 29% helix, 26% strand | — |
| B, C, D, E, F | Anind | protein | 452 | 29% helix, 27% strand | — |
Ligands and binding sites
- 4LU · 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-yl)-D-ribitol · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
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 | 1068 | 0.81 | 0.82 | 59 | empty |
| 2 | 1065 | 0.80 | 0.81 | 66 | 4LU |
| 3 | 1049 | 0.79 | 0.81 | 64 | 4LU |
| 4 | 996 | 0.79 | 0.80 | 63 | 4LU |
| 5 | 1017 | 0.78 | 0.80 | 63 | 4LU |
Interfaces
12 interfaces between chains.
- D–F · 3602 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 3600 Ų buried · 46 hydrogen bonds · protein-protein
- C–E · 3599 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 1295 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1291 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7P9Q · Crystal structure of Indole 3-Carboxylic acid decarboxylase from Arthrobacter nicotianae… · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 7P9Q · PDBe 7P9Q
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