MolNFT v1 · #165008 · protein
NADP dependent methylene-tetrahydromethanopterin dehydrogenase-NADP+- methenyl-H4MPT+ complex
6TGE · Bifunctional NADP-dependent methylenetetrahydromethanopterin…: “NADP dependent methylene-tetrahydromethanopterin dehydrogenase-NADP+- methenyl-H4MPT+ complex”. X-ray diffraction, 3 ligands (NAP, H4M, SO4), 20 pockets (best…
- PDB
- 6TGE
- Type
- protein
- Length
- 6,888 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional NADP-dependent methylenetetrahydromethanopterin…
- EC
- 1.5.1.-
- UniProt
- A0A1P8QVR4
- Ligands
- NAP, H4M, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | Bifunctional NADP-dependent methylenetetrahydromethanopterin DEHYDROGENASE/METHYLENETETRAHYDROFOLATE dehydrogenase (EC 1.5.1.-) | protein | 287 | 44% helix, 21% strand | A0A1P8QVR4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- H4M · 5,10-dimethylene tetrahydromethanopterin · ligand · 24 copies · chains A, C, B, D, F, E, L, G, I, H, J, K, M, O, N, P, R, Q, S, U, T, V, X, W
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
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 | 1164 | 0.79 | 0.81 | 99 | empty |
| 2 | 385 | 0.76 | 0.86 | 40 | SO4 |
| 3 | 925 | 0.76 | 0.79 | 66 | empty |
| 4 | 370 | 0.75 | 0.86 | 41 | SO4 |
| 5 | 353 | 0.75 | 0.86 | 39 | SO4 |
Interfaces
44 interfaces between chains.
- G–I · 794 Ų buried · 7 hydrogen bonds · protein-protein
- V–X · 784 Ų buried · 7 hydrogen bonds · protein-protein
- M–O · 763 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 762 Ų buried · 9 hydrogen bonds · protein-protein
- P–R · 761 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6TGE · NADP dependent methylene-tetrahydromethanopterin dehydrogenase-NADP+-methenyl-H4MPT+… · 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
- Every structure of UniProt A0A1P8QVR4
- Elsewhere: RCSB PDB 6TGE · PDBe 6TGE · UniProt A0A1P8QVR4
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