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Crystal structure of the complex between thrombin and the central "E" region of fibrin

Analyse Crystal structure of the complex between thrombin and the central "E" region of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2A45
Type: protein
Length: 864 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin light chain; Thrombin heavy chain; Fibrinogen alpha chain; Fibrinogen beta…
EC: 3.4.21.5
UniProt: P00734, P02671, P02675, P02679
Ligands: 0G6, PO4
Pockets: 16 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 30% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Thrombin light chain (EC 3.4.21.5)	protein	32	19% helix, 0% strand	P00734
B, E	Thrombin heavy chain (EC 3.4.21.5)	protein	258	13% helix, 28% strand	P00734
G, J	Fibrinogen alpha chain	protein	48	52% helix, 4% strand	P02671
H, K	Fibrinogen beta chain	protein	52	50% helix, 12% strand	P02675
I	Fibrinogen gamma chain	protein	40	58% helix, 8% strand	P02679
L	Fibrinogen gamma chain	protein	44	59% helix, 2% strand	P02679

Ligands and binding sites

0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · 2 copies · chains B, E
PO4 · Phosphate ion · ion · 2 copies · chains B, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1177	0.77	0.79	114	0G6, PO4
2	79	0.63	0.90	23	empty
3	140	0.61	0.84	24	empty
4	128	0.60	0.84	20	empty
5	298	0.58	0.77	47	0G6, PO4

Interfaces

22 interfaces between chains.

A–B · 1143 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 1096 Å² buried · 26 hydrogen bonds · protein-protein
H–J · 726 Å² buried · 9 hydrogen bonds · protein-protein
I–L · 721 Å² buried · 4 hydrogen bonds · protein-protein
G–K · 705 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 19 disulfide, 4 covalent (disulfide, covalent ligand).

Compared structures

2A45 · Crystal structure of the complex between thrombin and the central "E" region of fibrin · the same entry in another collection · chain L against L, TM-score 1.00
P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P02671
Every structure of UniProt P02675
Every structure of UniProt P02679
Elsewhere: RCSB PDB 2A45 · PDBe 2A45 · UniProt P00734 · UniProt P02671 · UniProt P02675 · UniProt P02679

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