Research workbench
X-ray crystal structure of the FORMYLTRANSFERASE/HYDROLASE complex (fhcabcd) from methylorubrum extorquens in complex with methylofuran
Analyse X-ray crystal structure of the FORMYLTRANSFERASE/HYDROLASE complex (fhcabcd)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S6Y
- Type
- protein
- Length
- 5,900 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formylmethanofuran dehydrogenase subunit a; Tungsten-containing formylmethanofuran…
- EC
- 2.3.1.101
- UniProt
- A9W3R9, A9W3S0, A9W3R7, A9W3R8
- Ligands
- DGL, GLU, IAS, MFN, L6K, K, ZN, CA, NA, CL, NH2
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 9 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formylmethanofuran dehydrogenase subunit a | protein | 548 | 35% helix, 22% strand | A9W3R9 |
| B | Tungsten-containing formylmethanofuran dehydrogenase, subunit B | protein | 356 | 39% helix, 21% strand | A9W3S0 |
| C, K, O | Formylmethanofuran dehydrogenase subunit C | protein | 267 | 13% helix, 27% strand | A9W3R7 |
| D, H, L, P | Formylmethanofuran--tetrahydromethanopterin formyltransferase (EC 2.3.1.101) | protein | 308 | 27% helix, 36% strand | A9W3R8 |
| E | Formylmethanofuran dehydrogenase subunit a | protein | 542 | 35% helix, 23% strand | A9W3R9 |
| F, J, N | Tungsten-containing formylmethanofuran dehydrogenase, subunit B | protein | 355 | 39% helix, 21% strand | A9W3S0 |
| G | Formylmethanofuran dehydrogenase subunit C | protein | 265 | 13% helix, 26% strand | A9W3R7 |
| I | Formylmethanofuran dehydrogenase subunit a | protein | 545 | 35% helix, 23% strand | A9W3R9 |
| M | Formylmethanofuran dehydrogenase subunit a | protein | 546 | 35% helix, 23% strand | A9W3R9 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 7 copies · chains A, B, C, D, I, K, J, L, O, P
- GLU · Glutamic acid · ligand · 3 copies · chains I, K, J, L
- IAS · Beta-L-aspartic acid · ligand · 2 copies · chains C, D, O, P
- MFN · N-[4,5,7-tricarboxyheptanoyl]-L-gamma-glutamyl-N-{2-[4-({5-[(formylamino)methyl]-3-furyl}methoxy) phenyl]ethyl}-D-glutamine · ligand · chains A
- L6K · (2~{S})-3-[4-[[5-(aminomethyl)furan-3-yl]methoxy]phenyl]-2-(methylamino)propanoic acid · ligand · chains I
- K · Potassium ion · metal · 9 copies · chains A, D, H, I, J, K, L, P
- ZN · Zinc ion · metal · 8 copies · chains A, E, I, M
- CA · Calcium ion · metal · 6 copies · chains A, B, L, P
- NA · Sodium ion · metal · chains J
- CL · Chloride ion · ion · 5 copies · chains A, B, C, I, J, K
- NH2 · Amino group · ion · chains A, B, C
- FMT · Formic acid · additive · 3 copies · chains A, I, J
- GOL · Glycerol · additive · 2 copies · chains A, B, H
- EDO · 1,2-ethanediol · additive · chains I
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 | 706 | 0.85 | 0.89 | 81 | empty |
| 2 | 638 | 0.84 | 0.88 | 89 | FMT, CA |
| 3 | 593 | 0.84 | 0.89 | 76 | FMT, ZN |
| 4 | 571 | 0.83 | 0.89 | 73 | empty |
| 5 | 131 | 0.79 | 0.97 | 25 | empty |
Interfaces
29 interfaces between chains.
- D–H · 2884 Ų buried · 50 hydrogen bonds · protein-protein
- L–P · 2841 Ų buried · 49 hydrogen bonds · protein-protein
- M–N · 2368 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2363 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2325 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent, 4 modified, 1 d-amino (covalent ligand, carboxylation, D-amino acid).
Compared structures
- 6S6Y · X-ray crystal structure of the formyltransferase/hydrolase complex (FhcABCD) from… · the same entry in another collection · chain M against M, 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 A9W3R9
- Every structure of UniProt A9W3S0
- Every structure of UniProt A9W3R7
- Every structure of UniProt A9W3R8
- Elsewhere: RCSB PDB 6S6Y · PDBe 6S6Y · UniProt A9W3R9 · UniProt A9W3S0 · UniProt A9W3R7 · UniProt A9W3R8
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