9T00: Prothrombin

Crystal structure of prethrombin-2 with a peptide corresponding to the C-terminus of the heavy chain of factor Va. Determined by X-ray diffraction at 2.8 Å resolution. Released 12 Aug 2026.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,125
Mol. weight: 77.9 kDa
Released: 12 Aug 2026

Explore 9T00 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9T00 contains 35 α-helices and 42 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	283-286	4
α-helix	290-292	3
α-helix	300-302	3
α-helix	309-311	3
α-helix	313-315	3
β-strand	325-326	2	1
α-helix	327-328	2
β-strand	335-340	6	2
β-strand	346-352	7	2
β-strand	357-360	4	2
α-helix	362-365	4
β-strand	366-367	2	3
α-helix	368-370	3
β-strand	372-373	2	3
α-helix	376-378	3
β-strand	379-383	5	2
β-strand	387	1	4
β-strand	397-399	3	2
β-strand	401-406	6	2
β-strand	411	1	5
β-strand	417	1	5
β-strand	421-425	5	2
α-helix	437-438	2
β-strand	439	1	1
α-helix	443-449	7
β-strand	455-460	6	1
α-helix	463-468	6
β-strand	479	1	4
β-strand	481-487	7	1
α-helix	488-489	2
α-helix	490-495	6
β-strand	505-508	4	1
α-helix	524	1
β-strand	528-532	5	1
β-strand	539-545	7	1
β-strand	558-562	5	1
α-helix	564-566	3
α-helix	567-575	9

Chains B and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	693-705	13

Chain C: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	283-286	4
α-helix	290-292	3
α-helix	300-302	3
α-helix	308-311	4
β-strand	325-326	2	6
α-helix	327-328	2
β-strand	335-340	6	7
β-strand	345-352	8	7
β-strand	357-360	4	7
α-helix	362-365	4
β-strand	366-367	2	8
α-helix	368-370	3
β-strand	372-373	2	8
α-helix	376-378	3
β-strand	379-383	5	7
β-strand	387	1	9
β-strand	397-399	3	7
β-strand	401-406	6	7
β-strand	411	1	10
β-strand	417	1	10
β-strand	421-425	5	7
α-helix	437-438	2
β-strand	439	1	6
α-helix	443-449	7
β-strand	455-460	6	6
α-helix	463-468	6
β-strand	479	1	9
β-strand	481-487	7	6
α-helix	488-489	2
α-helix	490-495	6
β-strand	505-508	4	6
α-helix	524	1
β-strand	528-532	5	6
β-strand	539-545	7	6
β-strand	558-562	5	6
α-helix	564-566	3
α-helix	567-575	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prothrombin	A, C	protein	314	Homo sapiens	P00734 (AlphaFold model)
Coagulation factor V heavy chain	B, D	protein	24	Homo sapiens	P12259 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9T00_1 Prothrombin (chains A, C)
MAIEGRTATSEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGRIVEGS
DAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGK
HSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRET
AASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNM
FCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFR
LKKWIQKVIDQFGE

Sequence of entity 2 (B, D), FASTA

>9T00_2 Coagulation factor V heavy chain (chains B, D)
EPEDEESDADYDYQNRLAAALGIR

Primary citation

Prothrombinase processivity is conferred by substrate allostery. Ustok, F.I., Faille, A., Warren, A.J. et al. EMBO J (2026) 45:3954-3977. DOI 10.1038/s44318-026-00782-4 · PubMed

Other PDB entries of the same protein (UniProt P00734 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5AFY 1.12 Å, Thrombin in complex with 3-chloro-benzamide
4UD9 1.12 Å, Thrombin in complex with 5-chlorothiophene-2-carboxamide
4UE7 1.13 Å, Thrombin in complex with 1-amidinopiperidine
4UDW 1.16 Å, Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2,…
4UEH 1.16 Å, Thrombin in complex with benzamidine
5AF9 1.18 Å, Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide
3RM2 1.23 Å, Human Thrombin in complex with MI003
5AHG 1.24 Å, Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine
2BVR 1.25 Å, Human thrombin complexed with fragment-based small molecules occupying the S1 pocket
3VXE 1.25 Å, Human alpha-thrombin-Bivalirudin complex at PD5.0
2UUF 1.26 Å, Thrombin-hirugen binary complex at 1.26A resolution
3SI4 1.27 Å, Human Thrombin In Complex With UBTHR104

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