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Thrombin complexed with fibrinopeptide a alpha (residues 7- 19). three complexes, one with epsilon-thrombin and two with alpha-thrombin

Analyse Thrombin complexed with fibrinopeptide a alpha (residues 7- 19). three… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1UCY
Type: protein
Length: 920 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin; Fibrinopeptide a-alpha
EC: 3.4.21.5
UniProt: P00735, P12803
Ligands: ACE
Pockets: 10 · best druggability 0.76

Structure

x-ray diffraction · 6 distinct chains · 15% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, J, M	Thrombin (EC 3.4.21.5)	protein	36	17% helix, 0% strand	P00735
H	Thrombin (EC 3.4.21.5)	protein	150	11% helix, 37% strand	P00735
E	Thrombin (EC 3.4.21.5)	protein	109	19% helix, 30% strand	P00735
F, I	Fibrinopeptide a-alpha	protein	12	25% helix, 17% strand	P12803
K, N	Thrombin (EC 3.4.21.5)	protein	259	15% helix, 34% strand	P00735
G	Fibrinopeptide a-alpha	protein	11	0% helix, 18% strand	P12803

Ligands and binding sites

ACE · Acetyl group · ligand · 3 copies · chains F, K, G, N, I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	790	0.76	0.80	63	empty
2	124	0.49	0.80	27	empty
3	118	0.46	0.79	21	empty
4	71	0.44	0.81	17	empty
5	101	0.43	0.78	19	empty

Interfaces

13 interfaces between chains.

H–E · 3497 Å² buried · 61 hydrogen bonds · protein-protein
J–K · 1382 Å² buried · 30 hydrogen bonds · protein-protein
M–N · 1350 Å² buried · 26 hydrogen bonds · protein-protein
L–H · 1099 Å² buried · 15 hydrogen bonds · protein-protein
N–I · 853 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 3 covalent, 3 modified (disulfide, covalent ligand, nonstandard).

Compared structures

1UCY · Thrombin complexed with fibrinopeptide a alpha (residues 7-19). three complexes, one with… · 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 P00735
Every structure of UniProt P12803
Elsewhere: RCSB PDB 1UCY · PDBe 1UCY · UniProt P00735 · UniProt P12803

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