MolNFT v1 · #105653 · protein
Crystal structure of dodecameric iron-containing heptosyltransferase tibc in complex with ADP-D-beta-D-heptose at 3.9 ångström resolution
4RB4 · Glycosyltransferase tibc: “Crystal structure of dodecameric iron-containing heptosyltransferase tibc in complex with…”. X-ray diffraction, 2 ligands (AQH, FE), 20 pockets (best druggability 0.84). MolNFT v1 #105653 on GenesisL1: 3D…
- PDB
- 4RB4
- Type
- protein
- Length
- 4,619 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase tibc
- EC
- 2.4.-.-
- UniProt
- H5MH13
- Ligands
- AQH, FE
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 11 distinct chains · 23% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 390 | 24% helix, 23% strand | H5MH13 |
| L | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 374 | 22% helix, 18% strand | H5MH13 |
| C, I | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 389 | 25% helix, 22% strand | H5MH13 |
| D | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 381 | 21% helix, 22% strand | H5MH13 |
| E | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 390 | 22% helix, 22% strand | H5MH13 |
| H | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 385 | 23% helix, 21% strand | H5MH13 |
| B | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 383 | 23% helix, 21% strand | H5MH13 |
| F | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 384 | 22% helix, 21% strand | H5MH13 |
| G | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 389 | 25% helix, 22% strand | H5MH13 |
| J | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 385 | 23% helix, 23% strand | H5MH13 |
| A | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 380 | 23% helix, 23% strand | H5MH13 |
Ligands and binding sites
- AQH · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate · ligand · 12 copies · chains K, L, C, D, E, H, B, F, G, I, J, A
- FE · Fe (III) ion · metal · 12 copies · chains K, L, C, D, E, H, B, F, G, I, J, A
- EDO · 1,2-ethanediol · additive · 3 copies · chains C, I, J
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 | 1181 | 0.84 | 0.85 | 86 | empty |
| 2 | 1191 | 0.84 | 0.85 | 84 | EDO |
| 3 | 1200 | 0.84 | 0.85 | 79 | empty |
| 4 | 1190 | 0.84 | 0.85 | 79 | EDO |
| 5 | 1189 | 0.84 | 0.85 | 83 | empty |
Interfaces
12 interfaces between chains.
- G–I · 1419 Ų buried · 17 hydrogen bonds · protein-protein
- E–A · 1415 Ų buried · 20 hydrogen bonds · protein-protein
- C–H · 1408 Ų buried · 16 hydrogen bonds · protein-protein
- K–J · 1400 Ų buried · 19 hydrogen bonds · protein-protein
- L–D · 1397 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 4RB4 · Crystal structure of dodecameric iron-containing heptosyltransferase TibC in complex with… · 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 H5MH13
- Elsewhere: RCSB PDB 4RB4 · PDBe 4RB4 · UniProt H5MH13
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