Thrombin

Thrombin (Thr) is a serine protease. Prothrombin (PThr) is cleaved to form Thr in the coagulation cascade. Thr catalyzes the conversion of fibrinogen to the insoluble fibrin. Thr is comnposed of heavy chain (HC) and light chain (LC). Prethrombin-1 lacks 155 N-terminal residues of PThr and is composed of a single polypeptide chain. Prethrombin-2 is the product of proteolysis of prethrombin-1 by trypsin or by active factor X. P-PACK Thr is a chemicaly modified Thr with inactivated catalytic site and active anion binding site. Hirudin is the most potent natural inhibitor of Thr. For some more details see Serine Protease and Serine Proteases.

3D Structures of thrombin3D Structures of thrombin

Updated December 2011

ThrombinThrombin

3pmb - bThr HC + LC – bovine
3qgn - hThr HC (mutant) + LC – human
3r3g - hThr HC + LC
2hnt– hThr-γ HC + LC
3jz1, 3jz2, 2od3 - hThr HC + LC (mutant)
3gic - hThr HC + LC
3ee0, 2a0q, 1sg8, 1sgi, 1jou - hThr HC (mutant) + LC
3edx, 3hk3, 3hk6 - mThr HC (mutant) + LC – mouse
2ocv - mThr HC + LC

Thrombin complexesThrombin complexes

3pma – bThr HC + LC residues 336-364 + sucrose octasulfate
1dlk - bThr HC + LC + peptide inhibitor
3hki - mThr HC (mutant) + LC + proteinase-activated receptor 1 peptide
3hkj - hThr HC (mutant) + LC + proteinase-activated receptor 1 peptide
2pux - mThr HC + LC + proteinase-activated receptor 3 peptide
2pv9 - mThr HC (mutant) + LC + proteinase-activated receptor 4 peptide
1dm4 - mThr HC (mutant) + LC + fibrinogen peptide
1ycp, 1bbr – bThr-ε HC + LC + fibrinogen peptide
1ucy - bThr HC + LC + fibrinogen peptide
1fph - hThr HC + LC + fibrinogen peptide
3bv9 - hThr HC (mutant) + LC + peptide inhibitor
2a2x, 1eb1, 1h8i, 1h8d, 1dit, 1hbt - hThr HC + LC + peptide inhibitor
1g37, 1eoj, 1eol, 1nrn, 1nro, 1nrp, 1nrq, 1nrr, 1nrs - hThr HC + peptide inhibitor
1hlt - hThr HC + LC + thrombomodulin peptide
2ank - hThr HC + LC + peptide + inhibitor
1bhx, 1abj, 1ppb - hThr HC + LC + inhibitor
1uvs, 1uvt, 1uvu - bThr HC + LC + inhibitor
1etr, 1ets, 1ett – bThr-ε HC + LC + inhibitor
3dd2 - hThr HC + LC + RNA
1hao, 1hap, 1hut - hThr HC + LC + DNA
3bf6 - hThr HC + LC + suramin
1xmn - hThr HC + LC + heparin
2h9t - hThr HC + LC + suramin + PPACK
1z8i, 1z8j - hThr HC + LC (mutant) + PPACK
1sfq, 1shh, 2thf, 1thp, 1b7x - hThr HC (mutant) + LC + PPACK
1ook - hThr HC + LC + PPACK
2hpp, 2hpq - hThr HC + LC + PThr residues 214-292 + PPACK

Thrombin complexes containing hirudinThrombin complexes containing hirudin

3c27, 2zc9, 2zda, 2zdv, 3egk, 2r2m, 2v3h, 2v3o, 2pks, 3eq0, 3dt0, 3dux, 3da9, 3dhk, 2znk, 2zo3, 3d49, 2zhe, 2zhf, 2zhw, 2zg0, 2zfq, 2zfr, 2zhq, 2zi2, 2ziq, 2zff, 2zfp, 2zgb, 2zgx, 2zf0, 3biu, 3biv, 2uuj, 2uuk, 2jh0, 2jh5, 2jh6, 2gde, 2bxt, 2bxu, 2bvr, 2bvs, 2bvx, 2bdy, 2feq, 2c8w, 2c8x, 2c8y, 2c8z, 2c90, 2c93, 2cf8, 2cf9, 2anm, 2w7g, 2fes, 1ype, 1ypg, 1ypj, 1ypk, 1ypl, 1ypm, 1vzq, 1way, 1wbg, 1riw, 1mu6, 1mu8, 1mue, 1nzq, 1o0d, 1oyt, 1o2g, 1gj4, 1gj5, 1kts, 1ktt, 1ghv, 1ghw, 1ghx, 1ghy, 1c5n, 1c5o, 1c4y, 1d3d, 1d3p, 1d3q, 1d3t, 1c4u, 1c4v, 1c1u, 1c1v, 1c1w, 1qj1, 1qj6, 1qj7, 1qhr, 1qur, 1d4p, 1ba8, 1bb0, 1ca8, 1awf, 1awh, 1bcu, 1a61, 1a3b, 1a3e, 1a46, 1a5g, 1b5g, 1tbz, 1a4w, 1ay6, 1ae8, 1afe, 1ad8, 1ai8, 1aix, 1bmm, 1bmn, 1lhc, 1lhd, 1lhe, 1lhf, 1lhg, 1uma, 1aht, 1fpc, 1w7g, 3ldx, 3p17- hThr HC + LC + hirudin peptide + inhibitor
1zgi, 1zgv, 1zrb, 1z71, 1xm1, 1sl3, 1ta2, 1ta6, 1nm6, 1nt1, 1doj, 1d9i, 1d6w, 1qbv, 1tmu, 1dwb, 1dwc, 1dwd, 1dwe - hThr HC + hirudin peptide + inhibitor
1ny2, 8kme, 7kme, 1a2c, 1tom, 1hdt, 1tmt, 1tmb - hThr HC + LC + hirudin peptide + peptide inhibitor
3hat - hThr HC + LC + hirudin peptide + fibrinogen peptide
2uuf, 2pw8, 1no9, 1c5l, 1vr1, 4thn, 5gds, 1hxf, 1hxe, 1abi, 1hgt, 1ihs, 1iht, 1thr, 1ths, 2hgt - hThr HC + LC + hirudin peptide
1vit - bThr HC + LC + hirudin peptide

Thrombin complex with proteinThrombin complex with protein

2a45 - hThr HC + LC + fibrinogen α, β, γ chains
2a1d, 1nu7 – bThr HC + LC + staphylocoagulase
1tb6 - hThr HC + LC (mutant) + antithrombin
2b5t - hThr HC (mutant) + LC + antithrombin III (mutant)
1jmo - hThr HC (mutant) + LC + heparin cofactor II
1e0f - hThr HC + LC + haemadin
1dx5 - hThr HC + LC + thrombomodulin
3p6z - hThr HC + LC + coagulation factor V
1de7 - hThr HC + LC + factor XIII activation peptide
3p70 - hThr HC + LC + factor V
3pmh - hThr HC + LC + platelet glycoprotein IB α chain
1avg - bThr HC + LC + triabin
1bth - bThr HC (mutant) + LC (mutant) + BPTI
1toc - bThr HC + LC + ornithodorin
1tbq, 1tbr - bThr HC + LC + rhodniin
1hrt - bThr HC + LC + hirudin
3htc, 4htc - hThr HC + LC + hirudin

ProthrombinProthrombin

3e6p, 2afq - hPThr HC + LC
3s7h, 3s7k– hPThr HC + LC (mutant)
3bei, 2pgb, 2gp9, 1tq0, 1rd3 - hPThr HC (mutant) + LC
1mh0 - hPThr HC (mutant)
1nl1, 1nl2, 2spt, 2pf1, 2pf2 – bPThr residues 1-156

Prothrombin complexesProthrombin complexes

3qdz – hPThr HC (mutant) + LC + proteinase-activated receptor 4 peptide
3lu9, 3bef - hPThr HC + LC (mutant) + proteinase-activated receptor 1 peptide
3k65 - hPThr HC residues 315-622 (mutant) + LC residues 199-314
3f68 - hPThr HC residues 364-622 + LC residues 328-363 + hirudin peptide
1jwt, 3c1k - hPThr HC + inhibitor
2pgq, 1tq7 - hPThr HC (mutant) + LC + PPACK
2cn0, 1t4u, 1t4v, 1sb1, 1k21, 1k22, 1g30, 1g32, 1o5g, 3tu7 - hPThr HC + LC + hirudin peptide + inhibitor
1twx - hPThr HC (mutant) + LC + hirudin peptide
2hwl - hPThr HC (mutant) + LC + fibrinogen γ’ peptide

Prothrombin complex with proteinProthrombin complex with protein

1id5 - hPThr HC + LC + ecotin
1p8v - hPThr HC + LC + platelet glycoprotein IB α chain
3gis - hPThr HC residues 364-622 (mutant) + LC residues 315-363 + thrombomodulin
3b9f - hPThr HC (mutant) + LC + protein C inhibitor
2ody - hPThr HC + LC + boophilin

Prethrombin-1Prethrombin-1

3nxp - hThr residues 199-622

Prethrombin-2Prethrombin-2

1nu9 – hThr HC + LC + staphylocoagulase
1mkw, 1mkx – bThr + Thr HC + LC
1hag, 1hah – hThr HC + LC + hirudin peptide
1hai – hThr HC + LC + inhibitor