MolNFT v1 · #97936 · protein
Fibrin-stabilizing factor with a bound ligand
4KTY · Coagulation factor xiii a chain: “Fibrin-stabilizing factor with a bound ligand”. X-ray diffraction, 4 ligands (DAS, 1TX, CA), 13 pockets (best druggability 0.62). MolNFT v1 #97936 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4KTY
- Type
- protein
- Length
- 1,405 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor xiii a chain; Peptide-like ligand
- EC
- 2.3.2.13
- UniProt
- P00488
- Ligands
- DAS, 1TX, CA, SO4
- Pockets
- 13 · 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 | 695 | 16% helix, 42% strand | P00488 |
| B | Coagulation factor xiii a chain (EC 2.3.2.13) | protein | 698 | 16% helix, 41% strand | P00488 |
| C, D | Peptide-like ligand | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- DAS · D-aspartic acid · ligand · 2 copies · chains A, C, B, D
- 1TX · (2S)-2-amino-7-methoxy-7-oxoheptanoic acid · ligand · 2 copies · chains A, C, B, D
- CA · Calcium ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 9 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.62 | 0.78 | 39 | GOL |
| 2 | 341 | 0.62 | 0.78 | 43 | GOL |
| 3 | 417 | 0.60 | 0.76 | 45 | GOL |
| 4 | 103 | 0.44 | 0.78 | 27 | ACY, DAS, 1TX |
| 5 | 86 | 0.42 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 755 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 465 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 458 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 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 4KTY · PDBe 4KTY · UniProt P00488
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