3H32: D-dimer from human fibrin

Crystal structure of D-dimer from human fibrin complexed with Gly-His-Arg-Pro-Tyr-amide. Determined by X-ray diffraction at 3.6 Å resolution. Released 28 Jul 2009.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 8
Atoms: 11,246
Mol. weight: 225.79 kDa
Ligands: CA
Released: 28 Jul 2009

Explore 3H32 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3H32 contains 51 α-helices and 96 β-strands across 8 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 D: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	125-128	4
α-helix	131-160	30
α-helix	161-163	3
β-strand	165	1	1
α-helix	175-187	13

Chain B: 12 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	153-155	3
α-helix	156-159	4
α-helix	161-192	32
β-strand	196	1	1
β-strand	198-199	2	2
α-helix	202-203	2
β-strand	204	1	3
β-strand	208	1	4
α-helix	211-215	5
β-strand	224-227	4	4
β-strand	236-241	6	4
β-strand	249-254	6	4
α-helix	267-271	5
β-strand	273-274	2	4
β-strand	278-280	3	5
β-strand	283-288	6	5
β-strand	292-293	2	4
α-helix	296-303	8
β-strand	308-315	8	4
β-strand	321-326	6	4
β-strand	328	1	6
α-helix	331-333	3
α-helix	334-336	3
β-strand	343	1	6
β-strand	347-348	2	4
α-helix	352-355	4
α-helix	362-364	3
β-strand	376	1	7
β-strand	377	1	8
β-strand	380	1	8
α-helix	394-397	4
β-strand	402	1	7
β-strand	407	1	9
β-strand	421	1	10
β-strand	445	1	10
β-strand	449-456	8	4

Chain C: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	99-106	8
α-helix	107-134	28
β-strand	140-141	2	2
β-strand	150	1	11
α-helix	153-156	4
β-strand	166-169	4	11
β-strand	178-181	4	11
β-strand	182-183	2	12
β-strand	191-192	2	12
β-strand	195-197	3	13
α-helix	208-213	6
β-strand	215-216	2	13
β-strand	217	1	3
β-strand	226-227	2	13
α-helix	230-238	9
β-strand	244-247	4	14
β-strand	248-251	4	13
β-strand	257-258	2	13
β-strand	261-265	5	14
β-strand	267	1	15
α-helix	270-272	3
β-strand	276	1	15
β-strand	281	1	14
α-helix	289-291	3
α-helix	310-312	3
β-strand	313-314	2	16
β-strand	317	1	16
α-helix	326-329	4
β-strand	333-334	2	16
β-strand	381-384	4	13
β-strand	387-388	2	14

Chain E: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	153-155	3
α-helix	156-192	37
β-strand	196	1	17
β-strand	198-199	2	18
β-strand	204	1	19
β-strand	208	1	20
α-helix	211-215	5
β-strand	224-227	4	20
β-strand	236-241	6	20
β-strand	249-255	7	20
α-helix	266-271	6
β-strand	272-274	3	20
β-strand	278-280	3	21
β-strand	283-288	6	21
β-strand	292-294	3	20
α-helix	296-303	8
β-strand	308-311	4	20
β-strand	314-315	2	20
β-strand	321-322	2	20
β-strand	325-326	2	20
β-strand	328	1	22
α-helix	334-336	3
β-strand	343	1	22
α-helix	362-364	3
β-strand	376	1	23
β-strand	377	1	24
β-strand	380	1	24
α-helix	394-397	4
β-strand	402	1	23
β-strand	407	1	25
β-strand	421	1	26
α-helix	424-426	3
β-strand	445	1	26
β-strand	449-456	8	20

Chain F: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	98-100	3
α-helix	103-106	4
α-helix	107-134	28
α-helix	138-139	2
β-strand	140-141	2	18
β-strand	145-150	6	27
α-helix	153-156	4
β-strand	166-169	4	27
β-strand	178-181	4	27
β-strand	182-184	3	28
β-strand	190-192	3	28
β-strand	195-197	3	29
α-helix	208-212	5
β-strand	215-216	2	29
β-strand	217	1	19
β-strand	226-227	2	29
α-helix	230-238	9
β-strand	244-251	8	29
β-strand	257-258	2	29
β-strand	261-263	3	29
β-strand	267	1	30
α-helix	270-272	3
β-strand	276	1	30
β-strand	280-281	2	29
α-helix	289-291	3
α-helix	301-303	3
β-strand	313	1	31
β-strand	314	1	32
β-strand	317	1	32
α-helix	326-329	4
β-strand	334	1	31
α-helix	356-358	3
β-strand	381-388	8	29
α-helix	389-391	3

Chains M and N: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fibrinogen alpha chain	A, D	protein	197	Homo sapiens	P02671 (AlphaFold model)
Fibrinogen beta chain	B, E	protein	458	Homo sapiens	P02675 (AlphaFold model)
Fibrinogen gamma chain, isoform gamma-A	C, F	protein	317	Homo sapiens	P02679 (AlphaFold model)
Fibrin B knob pentapeptide	M, N	protein	5		P02676 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>3H32_1 Fibrinogen alpha chain (chains A, D)
ADSGEGDFLAEGGGVRGPRVVERHQSACKDSDWPFCSDEDWNYKCPSGCRMKGLIDEVNQ
DFTNRINKLKNSLFEYQKNNKDSHSLTTNIMEILRGDFSSANNRDNTYNRVSEDLRSRIE
VLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALAREVDLKDYED
QQKQLEQVIAKDLLPSR

Sequence of entity 2 (B, E), FASTA

>3H32_2 Fibrinogen beta chain (chains B, E)
QGVNDNEEGFFSARGHRPLDKKREEAPSLRPAPPPISGGGYRARPAKAAATQKKVERKAP
DAGGCLHADPDLGVLCPTGCQLQEALLQQERPIRNSVDELNNNVEAVSQTSSSSFQYMYL
LKDLWQKRQKQVKDNENVVNEYSSELEKHQLYIDETVNSNIPTNLRVLRSILENLRSKIQ
KLESDVSAQMEYCRTPCTVSCNIPVVSGKECEEIIRKGGETSEMYLIQPDSSVKPYRVYC
DMNTENGGWTVIQNRQDGSVDFGRKWDPYKQGFGNVATNTDGKNYCGLPGEYWLGNDKIS
QLTRMGPTELLIEMEDWKGDKVKAHYGGFTVQNEANKYQISVNKYRGTAGNALMDGASQL
MGENRTMTIHNGMFFSTYDRDNDGWLTSDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGG
QYTWDMAKHGTDDGVVWMNWKGSWYSMRKMSMKIRPFF

Sequence of entity 3 (C, F), FASTA

>3H32_3 Fibrinogen gamma chain, isoform gamma-A (chains C, F)
KYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHDITGKDCQ
DIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKNWIQYKEG
FGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKVGPEADKY
RLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCAEQDGSGW
WMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKIIPFNRLTI
GEGQQHHLGGAKQAGDV

Sequence of entity 4 (M, N), FASTA

>3H32_4 Fibrin B knob pentapeptide (chains M, N)
GHRPY

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

Primary citation

Two families of synthetic peptides that enhance fibrin turbidity and delay fibrinolysis by different mechanisms. Pandi, L., Kollman, J.M., Lopez-Lira, F. et al. Biochemistry (2009) 48:7201-7208. DOI 10.1021/bi900647g · PubMed

Other PDB entries of the same protein (UniProt P02671 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5CFA 1.45 Å, Crystal structures of Bbp from Staphylococcus aureus with peptide ligand
4F27 1.92 Å, Crystal structures reveal the multi-ligand binding mechanism of the Staphylococcus…
1FZD 2.1 Å, Structure of recombinant alphaec domain from human fibrinogen-420
1BBR 2.3 Å, The structure of residues 7-16 of the a alpha chain of human fibrinogen bound to bovine…
1FZC 2.3 Å, Crystal structure of fragment double-D from human fibrin with two different bound ligands
3E1I 2.3 Å, Crystal Structure of BbetaD432A Variant Fibrinogen Fragment D with the Peptide Ligand…
2OYH 2.4 Å, Crystal Structure of Fragment D of gammaD298,301A Fibrinogen with the Peptide Ligand…
1RE3 2.45 Å, Crystal Structure of Fragment D of BbetaD398A Fibrinogen with the Peptide Ligand…
1DM4 2.5 Å, SER195ALA mutant of human thrombin complexed with fibrinopeptide a (7-16)
1FPH 2.5 Å, The interaction of thrombin with fibrinogen: a structural basis for its specificity
1FZG 2.5 Å, Crystal structure of fragment D from human fibrinogen with the peptide ligand…
1YCP 2.5 Å, The crystal structure of fibrinogen-aa peptide 1-23 (F8Y) bound to bovine thrombin…

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