MolNFT v1 · #126926 · protein
Fxiiia in complex with the inhibitor MI0621
5MHL · Coagulation factor xiii a chain: “Fxiiia in complex with the inhibitor MI0621”. X-ray diffraction, 4 ligands (7NX, CA, SO4), 11 pockets (best druggability 0.62). MolNFT v1 #126926 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5MHL
- Type
- protein
- Length
- 1,403 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor xiii a chain; Inhibitor MI0621
- EC
- 2.3.2.13
- UniProt
- P00488
- Ligands
- 7NX, CA, SO4, NH2
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor xiii a chain (EC 2.3.2.13) | protein | 692 | 16% helix, 41% strand | P00488 |
| B | Coagulation factor xiii a chain (EC 2.3.2.13) | protein | 697 | 16% helix, 42% strand | P00488 |
| K, O | Inhibitor MI0621 | protein | 7 | 0% helix, 43% strand | — |
Ligands and binding sites
- 7NX · Cyclohexylmethyl hydrogen carbonate · ligand · 2 copies · chains A, K, B, O
- CA · Calcium ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains A, K, B, O
- GOL · Glycerol · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.62 | 0.77 | 48 | GOL |
| 2 | 343 | 0.61 | 0.78 | 42 | GOL |
| 3 | 390 | 0.59 | 0.76 | 42 | empty |
| 4 | 102 | 0.45 | 0.79 | 24 | empty |
| 5 | 102 | 0.44 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 723 Ų buried · 6 hydrogen bonds · protein-protein
- B–O · 499 Ų buried · 9 hydrogen bonds · protein-protein
- A–K · 473 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
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 P00488
- Elsewhere: RCSB PDB 5MHL · PDBe 5MHL · UniProt P00488
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