3PMA: Thrombin light chain

2.2 Angstrom crystal structure of the complex between Bovine Thrombin and Sucrose Octasulfate. Determined by X-ray diffraction at 2.2 Å resolution. Released 20 Jul 2011.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Bos taurus
Chains: 4
Atoms: 4,798
Mol. weight: 68.9 kDa
Ligands: CIT
Released: 20 Jul 2011

Explore 3PMA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PMA contains 29 α-helices and 44 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.

Chains A and C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14C-14J	8

Chain B: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-36	7	3
β-strand	38-46	9	3
β-strand	51-54	4	3
α-helix	56-58	3
β-strand	60-60A	2	4
α-helix	60B-60D	3
β-strand	60F-60G	2	4
β-strand	64-68	5	3
β-strand	81-83	3	3
β-strand	85-90	6	3
β-strand	95	1	5
β-strand	100	1	5
β-strand	104-108	5	3
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	2
β-strand	156-162	7	2
α-helix	165-170	6
α-helix	175-177	3
β-strand	180-183	4	2
α-helix	184A-185	2
β-strand	189	1	1
β-strand	198-202	5	2
β-strand	207-215	9	2
β-strand	226-230	5	2
α-helix	232-234	3
α-helix	235-242	8

Chain D: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	6
β-strand	20-21	2	7
α-helix	22-23	2
β-strand	30-35	6	8
β-strand	39-46	8	8
β-strand	51-54	4	8
α-helix	56-58	3
β-strand	60-60A	2	9
α-helix	60B-60D	3
β-strand	60F-60G	2	9
α-helix	61-63	3
β-strand	64-68	5	8
β-strand	72	1	10
β-strand	81-83	3	8
β-strand	85-90	6	8
β-strand	95	1	11
β-strand	100	1	11
β-strand	104-108	5	8
α-helix	112-114	3
α-helix	120-121	2
β-strand	122	1	7
α-helix	123-124	2
α-helix	126-129C	7
β-strand	135-140	6	7
α-helix	149C-150	4
β-strand	154	1	10
β-strand	156-162	7	7
α-helix	165-170	6
β-strand	180-183	4	7
α-helix	184A-185	2
β-strand	189	1	6
β-strand	198-202	5	7
β-strand	207-215	9	7
β-strand	226-230	5	7
α-helix	232-234	3
α-helix	235-242	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin light chain	A, C	protein	29	Bos taurus	P00735 (AlphaFold model)
Thrombin heavy chain	B, D	protein	259	Bos taurus	P00735 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3PMA_1 Thrombin light chain (chains A, C)
EADCGLRPLFEKKQVQDQTEKELFESYIE

Sequence of entity 2 (B, D), FASTA

>3PMA_2 Thrombin heavy chain (chains B, D)
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLL
VRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCL
PDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIR
ITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDRLGS

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	2

Water and common crystallization additives (NA) are not listed.

Primary citation

Interaction of thrombin with sucrose octasulfate. Desai, B.J., Boothello, R.S., Mehta, A.Y. et al. Biochemistry (2011) 50:6973-6982. DOI 10.1021/bi2004526 · PubMed

Other PDB entries of the same protein (UniProt P00735 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7A0D 1.6 Å, The Crystal Structure of Bovine Thrombin in complex with Hirudin (C16U/C28U) at 1.6…
1NL1 1.9 Å, Bovine prothrombin fragment 1 in complex with calcium ion
7A0E 1.9 Å, The Crystal Structure of Bovine Thrombin in complex with Hirudin (C6U/C14U) at 1.9…
1ETR 2.2 Å, Refined 2.3 Å X-ray crystal structure of bovine thrombin complexes formed with the…
1MKX 2.2 Å, The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement…
1UCY 2.2 Å, Thrombin complexed with fibrinopeptide a alpha (residues 7-19). Three complexes, one…
2PF2 2.2 Å, The CA+2 ion and membrane binding structure of the gla domain of ca-prothrombin fragment 1
1BBR 2.3 Å, The structure of residues 7-16 of the a alpha chain of human fibrinogen bound to bovine…
1ETS 2.3 Å, Refined 2.3 Å X-ray crystal structure of bovine thrombin complexes formed with the…
1MKW 2.3 Å, The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement…
1NL2 2.3 Å, Bovine prothrombin fragment 1 in complex with calcium and lysophosphotidylserine
2ODY 2.35 Å, Thrombin-bound boophilin displays a functional and accessible reactive-site loop

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