MolNFT v1 · #128146 · protein
Human alpha thrombin complexed with anopheles gambiae CE5 anticoagulant
5NHU · Prothrombin: “Human alpha thrombin complexed with anopheles gambiae CE5 anticoagulant”. X-ray diffraction, 2 ligands (NAG, NA), 7 pockets (best druggability 0.81). MolNFT v1 #128146 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5NHU
- Type
- protein
- Length
- 913 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; AGAP008004-pa
- EC
- 3.4.21.5
- UniProt
- P00734, Q7Q3R9
- Ligands
- NAG, NA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 18% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 36 | 50% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 252 | 14% helix, 35% strand | P00734 |
| B | Prothrombin (EC 3.4.21.5) | protein | 33 | 36% helix, 0% strand | P00734 |
| A | Prothrombin (EC 3.4.21.5) | protein | 251 | 16% helix, 35% strand | P00734 |
| D | Prothrombin (EC 3.4.21.5) | protein | 29 | 34% helix, 0% strand | P00734 |
| C | Prothrombin (EC 3.4.21.5) | protein | 249 | 15% helix, 36% strand | P00734 |
| I | AGAP008004-pa | protein | 24 | 25% helix, 4% strand | Q7Q3R9 |
| J | AGAP008004-pa | protein | 29 | 21% helix, 3% strand | Q7Q3R9 |
| K | AGAP008004-pa | protein | 10 | 0% helix, 0% strand | Q7Q3R9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains H, A, C
- NA · Sodium ion · metal · 3 copies · chains H, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.81 | 0.85 | 72 | empty |
| 2 | 612 | 0.70 | 0.78 | 82 | empty |
| 3 | 107 | 0.58 | 0.85 | 22 | empty |
| 4 | 129 | 0.44 | 0.76 | 27 | empty |
| 5 | 59 | 0.41 | 0.82 | 25 | NA |
Interfaces
16 interfaces between chains.
- A–J · 1539 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 1510 Ų buried · 27 hydrogen bonds · protein-protein
- L–H · 1402 Ų buried · 29 hydrogen bonds · protein-protein
- B–A · 1278 Ų buried · 26 hydrogen bonds · protein-protein
- D–C · 1163 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5NHU · HUMAN ALPHA THROMBIN COMPLEXED WITH ANOPHELES GAMBIAE cE5 ANTICOAGULANT · the same entry in another collection · chain L against L, 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 P00734
- Every structure of UniProt Q7Q3R9
- Elsewhere: RCSB PDB 5NHU · PDBe 5NHU · UniProt P00734 · UniProt Q7Q3R9
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