MolNFT v1 · #105639 · protein
Crystal structure of bacterial iron-containing dodecameric glycosyltransferase tibc from enterotoxigenic E.COLI H10407
4RAP: “Crystal structure of bacterial iron-containing dodecameric glycosyltransferase tibc from enterotoxigenic…”. X-ray diffraction, 1 ligand (FE), 20 pockets (best druggability 0.86). MolNFT v1 #105639 on GenesisL1: 3D structure, binding…
- PDB
- 4RAP
- Type
- protein
- Length
- 4,613 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase tibc
- EC
- 2.4.-.-
- UniProt
- Q9S4K6
- Ligands
- FE
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 10 distinct chains · 25% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 381 | 25% helix, 22% strand | Q9S4K6 |
| B | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 383 | 25% helix, 20% strand | Q9S4K6 |
| C, I, K | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 389 | 25% helix, 22% strand | Q9S4K6 |
| D | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 381 | 24% helix, 22% strand | Q9S4K6 |
| E | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 390 | 25% helix, 21% strand | Q9S4K6 |
| F | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 382 | 25% helix, 17% strand | Q9S4K6 |
| G | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 389 | 25% helix, 19% strand | Q9S4K6 |
| H | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 385 | 25% helix, 22% strand | Q9S4K6 |
| J | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 384 | 25% helix, 21% strand | Q9S4K6 |
| L | Glycosyltransferase tibc (EC 2.4.-.-) | protein | 371 | 25% helix, 18% strand | Q9S4K6 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- EDO · 1,2-ethanediol · additive · 5 copies · chains C, I, F, J, L
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 | 1107 | 0.86 | 0.87 | 97 | EDO |
| 2 | 1126 | 0.86 | 0.87 | 92 | empty |
| 3 | 1083 | 0.85 | 0.86 | 93 | empty |
| 4 | 1064 | 0.85 | 0.86 | 89 | EDO |
| 5 | 1180 | 0.85 | 0.86 | 92 | EDO |
Interfaces
12 interfaces between chains.
- A–E · 1455 Ų buried · 17 hydrogen bonds · protein-protein
- G–I · 1454 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 1423 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 1404 Ų buried · 16 hydrogen bonds · protein-protein
- J–K · 1397 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4RAP · Crystal structure of bacterial iron-containing dodecameric glycosyltransferase TibC from… · the same entry in another collection · chain L against L, 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 Q9S4K6
- Elsewhere: RCSB PDB 4RAP · PDBe 4RAP · UniProt Q9S4K6
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