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3P6Z

Structural basis of thrombin mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A, D
(A, G)
Thrombin light chainpolymer364096.52UniProt (P00734)
Pfam (PF09396)
Homo sapiens (human)Coagulation factor II, Thrombin light chain
2B, E
(B, H)
Thrombin heavy chainpolymer25929780.22UniProt (P00734)
Pfam (PF00089)
Homo sapiens (human)Coagulation factor II, Thrombin heavy chain
3C, F
(C, I)
Coagulation factor Vpolymer718391.92UniProt (P12259)Homo sapiens (human)Activated protein C cofactor
4G, J, K, P, S...
(A, B, G, H)
SODIUM IONnon-polymer23.09Chemie (NA)
5H, Q
(B, H)
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamidenon-polymer454.02BIRD (PRD_000020)
Chemie (0G6)
6I, R
(B, H)
2-acetamido-2-deoxy-beta-D-glucopyranosenon-polymer221.22Chemie (NAG)
7L, M, N
(B)
CHLORIDE IONnon-polymer35.53Chemie (CL)
8O
(B)
(4S)-2-METHYL-2,4-PENTANEDIOLnon-polymer118.21Chemie (MPD)
9AA, BA, CA, X, Y...
(G, H, I, A, B...)
waterwater18.0505Chemie (HOH)
Sequence modifications
C, I: 657 - 709 (UniProt: P12259)
PDBExternal DatabaseDetails
Ala 639-expression tag
His 640-expression tag
His 641-expression tag
His 642-expression tag
His 643-expression tag
His 644-expression tag
His 645-expression tag
Val 646-expression tag
Gly 647-expression tag
Thr 648-expression tag
Trp 649-expression tag
Glu 650-expression tag
Asn 651-expression tag
Leu 652-expression tag
Tyr 653-expression tag
Phe 654-expression tag
Gln 655-expression tag
Ser 656-expression tag
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains6
Total formula weight84537.4
Non-Polymers*Number of molecules17
Total formula weight1781.8
All*Total formula weight86319.2
*Water molecules are not included.

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PDB entries from 2025-07-09

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