Research workbench
Crystal structure of cell surface glyceraldehyde-3-phosphate dehydrogenase complexed with NAD+ from lactobacillus plantarum
Analyse Crystal structure of cell surface glyceraldehyde-3-phosphate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IQM
- Type
- protein
- Length
- 1,336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase, type I
- EC
- 1.2.1.12
- UniProt
- D7VA33
- Ligands
- NAD
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate dehydrogenase, type I (EC 1.2.1.12) | protein | 339 | 29% helix, 28% strand | D7VA33 |
| B | Glyceraldehyde-3-phosphate dehydrogenase, type I (EC 1.2.1.12) | protein | 323 | 27% helix, 28% strand | D7VA33 |
| C | Glyceraldehyde-3-phosphate dehydrogenase, type I (EC 1.2.1.12) | protein | 334 | 30% helix, 27% strand | D7VA33 |
| D | Glyceraldehyde-3-phosphate dehydrogenase, type I (EC 1.2.1.12) | protein | 340 | 31% helix, 27% strand | D7VA33 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, D, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.79 | 0.81 | 111 | TRS |
| 2 | 1134 | 0.77 | 0.79 | 123 | NAD |
| 3 | 599 | 0.71 | 0.79 | 70 | NAD |
| 4 | 456 | 0.68 | 0.80 | 53 | NAD |
| 5 | 249 | 0.58 | 0.79 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2104 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2086 Ų buried · 50 hydrogen bonds · protein-protein
- B–D · 1407 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1393 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 448 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6IQM · Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with… · the same entry in another collection · chain B against B, 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 D7VA33
- Elsewhere: RCSB PDB 6IQM · PDBe 6IQM · UniProt D7VA33
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