3P70: Human alpha-thrombin, light chain

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. Determined by X-ray diffraction at 2.55 Å resolution. Released 28 Sept 2011.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 12
Atoms: 9,477
Mol. weight: 171.55 kDa
Ligands: NAG, BEN, BGC
Released: 28 Sept 2011

Explore 3P70 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3P70 contains 49 α-helices and 99 β-strands across 9 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, C and E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	343-345	3
α-helix	352-360	9

Chain B: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	365	1	1
β-strand	368-369	2	2
α-helix	370-371	2
β-strand	378-383	6	3
β-strand	388-397	10	3
β-strand	400-403	4	3
α-helix	405-407	3
β-strand	409-410	2	4
α-helix	411-413	3
β-strand	415-416	2	4
α-helix	419-421	3
β-strand	422-426	5	3
β-strand	430	1	5
β-strand	440-449	10	3
β-strand	454	1	6
β-strand	460	1	6
β-strand	464-468	5	3
α-helix	471-474	4
β-strand	475	1	7
β-strand	478	1	7
β-strand	482	1	2
α-helix	483-485	3
α-helix	486-492	7
β-strand	498-503	6	2
β-strand	522	1	5
β-strand	524-529	6	2
β-strand	530	1	8
α-helix	533-539	7
β-strand	548-551	4	8
α-helix	555-557	3
β-strand	562	1	1
β-strand	571-575	5	2
β-strand	582-587	6	2
β-strand	588-590	3	8
β-strand	601-604	4	8
α-helix	610-620	11

Chain D: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	365	1	9
β-strand	368-369	2	10
α-helix	370-371	2
β-strand	378-383	6	11
β-strand	388-395	8	11
β-strand	400-403	4	11
α-helix	405-407	3
β-strand	409-410	2	12
α-helix	411-413	3
β-strand	415-416	2	12
β-strand	422-426	5	11
β-strand	430	1	13
β-strand	440-442	3	11
β-strand	444-449	6	11
β-strand	454	1	14
β-strand	460	1	14
β-strand	464-468	5	11
α-helix	471-474	4
β-strand	475	1	15
β-strand	478	1	15
α-helix	480-481	2
β-strand	482	1	10
α-helix	483-484	2
α-helix	486-492	7
β-strand	498-503	6	10
β-strand	522	1	13
β-strand	524-531	8	10
α-helix	533-539	7
β-strand	548-551	4	10
α-helix	555-557	3
β-strand	562	1	9
β-strand	571-575	5	10
β-strand	582-590	9	10
β-strand	601-605	5	10
α-helix	606-617	12

Chain F: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	365	1	16
β-strand	368-369	2	17
α-helix	370-371	2
β-strand	378-383	6	18
β-strand	388-395	8	18
β-strand	400-403	4	18
α-helix	405-408	4
β-strand	409-410	2	19
α-helix	411-413	3
β-strand	415-416	2	19
α-helix	419-421	3
β-strand	422-426	5	18
β-strand	430	1	20
β-strand	440-442	3	18
β-strand	444-449	6	18
β-strand	454	1	21
β-strand	460	1	21
β-strand	464-468	5	18
α-helix	480-481	2
β-strand	482	1	17
α-helix	483-484	2
α-helix	486-492	7
β-strand	498-503	6	17
β-strand	522	1	20
β-strand	524-530	7	17
α-helix	533-539	7
β-strand	548-551	4	17
α-helix	555-557	3
β-strand	562	1	16
β-strand	571-575	5	17
β-strand	582-590	9	17
β-strand	601-605	5	17
α-helix	610-617	8

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	352-360	9

Chain H: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	365	1	22
β-strand	368-369	2	23
α-helix	370-371	2
β-strand	378-383	6	24
β-strand	388-395	8	24
β-strand	400-403	4	24
α-helix	405-407	3
β-strand	409	1	25
α-helix	411-413	3
β-strand	416	1	25
α-helix	419-421	3
β-strand	422-426	5	24
β-strand	430	1	26
β-strand	440-442	3	24
β-strand	444-449	6	24
β-strand	454	1	27
β-strand	460	1	27
β-strand	464-468	5	24
α-helix	471-474	4
α-helix	480-481	2
β-strand	482	1	23
α-helix	483-484	2
α-helix	486-492	7
β-strand	498-503	6	23
β-strand	522	1	26
β-strand	524-529	6	23
β-strand	530-531	2	28
α-helix	533-539	7
β-strand	548-551	4	28
α-helix	555-557	3
β-strand	562	1	22
β-strand	571-575	5	23
β-strand	582-587	6	23
β-strand	588-590	3	28
β-strand	601-604	4	28
α-helix	610-619	10

Chain M: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	668-670	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Human alpha-thrombin, light chain	A, C, E, G	protein	36	Homo sapiens	P00734 (AlphaFold model)
Human alpha-thrombin, heavy chain	B, D, F, H	protein	259	Homo sapiens	P00734 (AlphaFold model)
Human factor V, A2-B domain linker	M, N, O, P	protein	71	Homo sapiens	P12259 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>3P70_1 HUMAN ALPHA-THROMBIN, LIGHT CHAIN (chains A, C, E, G)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (B, D, F, H), FASTA

>3P70_2 HUMAN ALPHA-THROMBIN, HEAVY CHAIN (chains B, D, F, H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (M, N, O, P), FASTA

>3P70_3 HUMAN FACTOR V, A2-B DOMAIN LINKER (chains M, N, O, P)
AHHHHHHVGTWENLYFQSIPDDDEDSYEIFEPPESTVMATRKMHDRLEPEDEESDADYDY
QNRLAAALGIR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
BEN	Benzamidine	C7 H8 N2	4
BGC	beta-D-glucopyranose	C6 H12 O6	3

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

Primary citation

Structural basis of thrombin-mediated factor V activation: the Glu666-Glu672 sequence is critical for processing at the heavy chain-B domain junction. Corral-Rodriguez, M.A., Bock, P.E., Hernandez-Carvajal, E. et al. Blood (2011) 117:7164-7173. DOI 10.1182/blood-2010-10-315309 · 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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