Research workbench
Hmdii from desulfurobacterium thermolithotrophum reconstitued with fe- guanylylpyridinol (fegp) cofactor and co-crystallized with methenyl- tetrahydrofolate form a
Analyse Hmdii from desulfurobacterium thermolithotrophum reconstitued with fe… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HUY
- Type
- protein
- Length
- 1,413 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420-dependent N(5),N(10)- methenyltetrahydromethanopterin reductase-related…
- EC
- 1.12.98.2
- UniProt
- F0S2B6
- Ligands
- GUE, FE9
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coenzyme F420-dependent N(5),N(10)- methenyltetrahydromethanopterin reductase-related protein (EC 1.12.98.2) | protein | 350 | 56% helix, 11% strand | F0S2B6 |
| B | Coenzyme F420-dependent N(5),N(10)- methenyltetrahydromethanopterin reductase-related protein | protein | 357 | 59% helix, 11% strand | F0S2B6 |
| C | Coenzyme F420-dependent N(5),N(10)- methenyltetrahydromethanopterin reductase-related protein (EC 1.12.98.2) | protein | 351 | 56% helix, 11% strand | F0S2B6 |
| D | Coenzyme F420-dependent N(5),N(10)- methenyltetrahydromethanopterin reductase-related protein | protein | 355 | 58% helix, 11% strand | F0S2B6 |
Ligands and binding sites
- GUE · 5,10-Methenyltetrahydrofolate · ligand · 4 copies · chains A, B, C, D
- FE9 · iron-guanylyl pyridinol cofactor · ligand · 2 copies · chains A, C
- DMS · Dimethyl sulfoxide · additive · 9 copies · chains B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, D
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.80 | 0.83 | 87 | DMS |
| 2 | 434 | 0.76 | 0.85 | 50 | FE9, GUE |
| 3 | 486 | 0.75 | 0.83 | 48 | FE9, GUE |
| 4 | 475 | 0.73 | 0.82 | 47 | DMS, GUE |
| 5 | 467 | 0.72 | 0.82 | 50 | DMS, GUE |
Interfaces
6 interfaces between chains.
- A–B · 6711 Ų buried · 70 hydrogen bonds · protein-protein
- C–D · 6665 Ų buried · 66 hydrogen bonds · protein-protein
- B–D · 298 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 209 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 74 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6HUY · HmdII from Desulfurobacterium thermolithotrophum reconstitued with Fe-guanylylpyridinol… · the same entry in another collection · chain D against D, 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 F0S2B6
- Elsewhere: RCSB PDB 6HUY · PDBe 6HUY · UniProt F0S2B6
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