MolNFT v1 · #137527 · protein
Crystal structure of a transketolase from neisseria gonorrhoeae
5VRB: “Crystal structure of a transketolase from neisseria gonorrhoeae”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.76). MolNFT v1 #137527 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VRB
- Type
- protein
- Length
- 2,528 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transketolase
- EC
- 2.2.1.1
- UniProt
- B4RKU9
- Ligands
- CA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transketolase (EC 2.2.1.1) | protein | 627 | 48% helix, 13% strand | B4RKU9 |
| B | Transketolase (EC 2.2.1.1) | protein | 646 | 46% helix, 13% strand | B4RKU9 |
| C | Transketolase (EC 2.2.1.1) | protein | 615 | 46% helix, 13% strand | B4RKU9 |
| D | Transketolase (EC 2.2.1.1) | protein | 640 | 46% helix, 13% strand | B4RKU9 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.76 | 0.87 | 48 | CA |
| 2 | 404 | 0.72 | 0.83 | 48 | EDO, CA |
| 3 | 385 | 0.72 | 0.83 | 43 | CA |
| 4 | 480 | 0.70 | 0.81 | 61 | empty |
| 5 | 203 | 0.70 | 0.87 | 42 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3929 Ų buried · 69 hydrogen bonds · protein-protein
- C–D · 3822 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 470 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 57 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 5VRB · Crystal structure of a transketolase from Neisseria gonorrhoeae · the same entry in another collection · chain C against C, 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 B4RKU9
- Elsewhere: RCSB PDB 5VRB · PDBe 5VRB · UniProt B4RKU9
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