MolNFT v1 · #99291 · protein + DNA

X-ray structure of the complex between human thrombin and the tba deletion mutant lacking thymine 3 nucleobase

4LZ4 · Thrombin light chain: “X-ray structure of the complex between human thrombin and the tba deletion mutant lacking thymine 3 nucleobase”. X-ray diffraction, 4 ligands (0G6, NAG, NA), 9 pockets (best druggability 0.59). MolNFT v1…

PDB: 4LZ4
Type: protein + DNA
Length: 614 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin light chain; Thrombin heavy chain; Thrombin binding aptamer (tba)
EC: 3.4.21.5
UniProt: P00734
Ligands: 0G6, NAG, NA, K
Pockets: 9 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Thrombin light chain (EC 3.4.21.5)	protein	34	29% helix, 3% strand	P00734
B, D	Thrombin heavy chain (EC 3.4.21.5)	protein	258	15% helix, 34% strand	P00734
E, F	Thrombin binding aptamer (tba)	dna	15	—	—

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, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
NA · Sodium ion · metal · 2 copies · chains B, D
K · Potassium ion · metal · 2 copies · chains E, F

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	151	0.59	0.83	28	empty
2	236	0.56	0.78	35	0G6
3	219	0.55	0.78	30	0G6
4	109	0.37	0.74	22	empty
5	51	0.35	0.79	16	empty

Interfaces

7 interfaces between chains.

C–D · 1415 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1402 Å² buried · 36 hydrogen bonds · protein-protein
B–E · 552 Å² buried · 22 hydrogen bonds · protein-nucleic
D–F · 532 Å² buried · 15 hydrogen bonds · protein-nucleic
A–D · 268 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 covalent, 2 glycan, 2 modified (disulfide, covalent ligand, N-glycosylation, nucleotide modification).

Compared structures

4LZ4 · X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking… · the same entry in another collection · chain F against F, TM-score 1.00
P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain D 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
Elsewhere: RCSB PDB 4LZ4 · PDBe 4LZ4 · UniProt P00734

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