1DM4: SER195ALA mutant of human thrombin

SER195ALA mutant of human thrombin complexed with fibrinopeptide a (7-16). Determined by X-ray diffraction at 2.5 Å resolution. Released 19 Jan 2000.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,525
Mol. weight: 34.91 kDa
Released: 19 Jan 2000

Explore 1DM4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1DM4 contains 9 α-helices and 25 β-strands across 3 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: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1F	1	1
α-helix	8-10	3
α-helix	14C-14I	7

Chain B: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	2
β-strand	20-21	2	3
β-strand	30-35	6	4
β-strand	40-46	7	4
β-strand	51-54	4	4
α-helix	56-59	4
α-helix	60B-60D	3
β-strand	64-68	5	4
β-strand	72	1	5
β-strand	81-90	10	4
β-strand	95	1	6
β-strand	100	1	6
β-strand	104-108	5	4
α-helix	111-114	4
β-strand	122	1	3
β-strand	123	1	1
α-helix	126-129C	7
β-strand	135-140	6	3
β-strand	154	1	5
β-strand	156-163	8	3
α-helix	165-171	7
β-strand	180-183	4	3
α-helix	186-186B	3
β-strand	189	1	2
β-strand	195	1	7
β-strand	197	1	7
β-strand	198-202	5	3
β-strand	207-216	10	3
β-strand	226-230	5	3
α-helix	235-245	11

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	316-317	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (alpha thrombin:light chain)	A	protein	35	Homo sapiens	P00734 (AlphaFold model)
Protein (mutant alpha thrombin:heavy chain)	B	protein	260	Homo sapiens	P00734 (AlphaFold model)
Protein (fibrinopeptide)	C	protein	11		P02671 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1DM4_1 PROTEIN (ALPHA THROMBIN:LIGHT CHAIN) (chains A)
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDG

Sequence of entity 2 (B), FASTA

>1DM4_2 PROTEIN (MUTANT ALPHA THROMBIN:HEAVY CHAIN) (chains B)
RIVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDL
LVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVC
LPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRI
RITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGF
YTHVFRLKKWIQKVIDQFGE

Sequence of entity 3 (C), FASTA

>1DM4_3 PROTEIN (FIBRINOPEPTIDE) (chains C)
XDFLAEGGGVR

Primary citation

Structure of the Ser195Ala mutant of human alpha--thrombin complexed with fibrinopeptide A(7--16): evidence for residual catalytic activity. Krishnan, R., Sadler, J.E., Tulinsky, A. Acta Crystallogr D Biol Crystallogr (2000) 56:406-410. DOI 10.1107/S0907444900001487 · 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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