3P6Z: 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 1.7 Å resolution. Released 15 Jun 2011.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,445
Mol. weight: 86.32 kDa
Ligands: 0G6, NAG
Released: 15 Jun 2011

Explore 3P6Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3P6Z contains 30 α-helices and 46 β-strands across 6 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 G: 2 helices, 0 β-strands

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

Chain B: 12 helices, 22 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	388-395	8	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
α-helix	480-481	2
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	524-530	7	2
α-helix	533-538	6
β-strand	548-551	4	2
α-helix	555-557	3
β-strand	562	1	1
β-strand	571-575	5	2
β-strand	582-590	9	2
β-strand	601-605	5	2
α-helix	607-609	3
α-helix	610-620	11

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	668-671	4

Chain H: 12 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	365	1	7
β-strand	368-369	2	8
α-helix	370-371	2
β-strand	378-383	6	9
β-strand	388-395	8	9
β-strand	400-403	4	9
α-helix	405-407	3
β-strand	409-410	2	10
α-helix	411-413	3
β-strand	415-416	2	10
α-helix	419-421	3
β-strand	422-426	5	9
β-strand	430	1	11
β-strand	440-449	10	9
β-strand	454	1	12
β-strand	460	1	12
β-strand	464-468	5	9
α-helix	471-474	4
β-strand	475	1	13
β-strand	478	1	13
α-helix	480-481	2
β-strand	482	1	8
α-helix	483-485	3
α-helix	486-492	7
β-strand	498-503	6	8
β-strand	522	1	11
β-strand	524-530	7	8
α-helix	533-538	6
β-strand	548-551	4	8
α-helix	555-557	3
β-strand	562	1	7
β-strand	571-575	5	8
β-strand	582-590	9	8
β-strand	601-605	5	8
α-helix	607-609	3
α-helix	610-620	11

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	668-672	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thrombin light chain	A, G	protein	36	Homo sapiens	P00734 (AlphaFold model)
Thrombin heavy chain	B, H	protein	259	Homo sapiens	P00734 (AlphaFold model)
Coagulation factor V	C, I	protein	71	Homo sapiens	P12259 (AlphaFold model)

Sequence of entity 1 (A, G), FASTA

>3P6Z_1 Thrombin light chain (chains A, G)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Sequence of entity 2 (B, H), FASTA

>3P6Z_2 Thrombin heavy chain (chains B, H)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Sequence of entity 3 (C, I), FASTA

>3P6Z_3 Coagulation factor V (chains C, I)
AHHHHHHVGTWENLYFQSIPDDDEDSYEIFEPPESTVMATRKMHDRLEPEDEESDADYDY
QNRLAAALGIR

Ligands and cofactors

ID	Name	Formula	Copies
0G6	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexa…	C21 H34 Cl N6 O3	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Water and common crystallization additives (NA, CL, MPD) 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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