1FZC: Fibrin

Crystal structure of fragment double-D from human fibrin with two different bound ligands. Determined by X-ray diffraction at 2.3 Å resolution. Released 14 Oct 1998.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 10
Atoms: 11,594
Mol. weight: 171.32 kDa
Ligands: MAN, NAG, CA
Released: 14 Oct 1998

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

Secondary structure: helices and β-sheets

1FZC contains 52 α-helices and 107 β-strands across 10 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: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	120-124	5
α-helix	125-159	35
β-strand	165	1	1
α-helix	176-190	15

Chain B: 12 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	160-192	33
β-strand	196	1	1
β-strand	198-199	2	2
α-helix	202	1
β-strand	203-204	2	3
β-strand	208	1	4
α-helix	211-216	6
β-strand	223-227	5	4
α-helix	234-235	2
β-strand	236-241	6	4
α-helix	244-246	3
β-strand	249-255	7	4
α-helix	266-271	6
β-strand	273-274	2	4
β-strand	277-278	2	5
β-strand	288-289	2	5
β-strand	292-293	2	4
α-helix	296-304	9
β-strand	309-315	7	4
β-strand	321-331	11	4
α-helix	334-336	3
β-strand	340-347	8	4
α-helix	352-355	4
α-helix	362-366	5
α-helix	373-375	3
β-strand	376	1	6
β-strand	377	1	7
β-strand	380	1	7
β-strand	402	1	6
β-strand	407	1	8
β-strand	410	1	9
β-strand	421	1	10
β-strand	437	1	9
α-helix	438-441	4
β-strand	442	1	9
β-strand	445	1	10
β-strand	449-455	7	4

Chain C: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	103-134	32
α-helix	138-139	2
β-strand	140-141	2	2
β-strand	150	1	11
α-helix	153-157	5
β-strand	165-169	5	11
β-strand	178-184	7	11
β-strand	190-197	8	11
α-helix	208-213	6
β-strand	215-216	2	11
β-strand	217-218	2	3
β-strand	226-227	2	11
α-helix	230-237	8
β-strand	244-251	8	11
β-strand	257-263	7	11
β-strand	266-267	2	12
β-strand	271-274	4	13
β-strand	276-277	2	12
β-strand	280-281	2	11
α-helix	289-291	3
α-helix	301-304	4
α-helix	310-312	3
β-strand	313	1	14
β-strand	314	1	15
β-strand	317	1	15
α-helix	326-330	5
β-strand	334	1	14
β-strand	339	1	16
β-strand	342-343	2	17
β-strand	347	1	18
β-strand	353	1	19
α-helix	356-358	3
β-strand	366	1	18
β-strand	368-369	2	17
β-strand	377	1	19
β-strand	381-388	8	11

Chain E: 13 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	152-157	6
α-helix	160-192	33
β-strand	196	1	20
β-strand	198-199	2	21
α-helix	202	1
β-strand	203-204	2	22
β-strand	208	1	23
α-helix	211-216	6
β-strand	223-227	5	23
α-helix	234-235	2
β-strand	236-241	6	23
α-helix	244-246	3
β-strand	249-255	7	23
α-helix	266-271	6
β-strand	272-274	3	23
β-strand	277-278	2	24
β-strand	288-289	2	24
β-strand	292-294	3	23
α-helix	296-303	8
β-strand	309-315	7	23
β-strand	321-331	11	23
α-helix	334-336	3
β-strand	340-347	8	23
α-helix	352-355	4
α-helix	363-366	4
α-helix	373-375	3
β-strand	376	1	25
β-strand	377	1	26
β-strand	380	1	26
β-strand	402	1	25
β-strand	407	1	27
β-strand	410-411	2	28
β-strand	421	1	29
β-strand	436-437	2	28
α-helix	438-441	4
β-strand	442	1	28
β-strand	445	1	29
β-strand	449-455	7	23

Chain F: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	103-107	5
α-helix	110-133	24
α-helix	139	1
β-strand	140-141	2	21
β-strand	150	1	30
α-helix	153-158	6
β-strand	165-169	5	30
β-strand	178-184	7	30
β-strand	190-197	8	30
α-helix	208-213	6
β-strand	215-216	2	30
β-strand	217-218	2	22
β-strand	226-227	2	30
α-helix	230-237	8
β-strand	244-251	8	30
β-strand	257-263	7	30
β-strand	266-267	2	31
α-helix	270-272	3
β-strand	276-277	2	31
β-strand	280-283	4	30
α-helix	289-291	3
α-helix	310-312	3
β-strand	313	1	32
β-strand	314	1	33
β-strand	317	1	33
α-helix	326-330	5
β-strand	334	1	32
β-strand	339	1	34
β-strand	342-343	2	35
β-strand	347	1	36
β-strand	353	1	37
α-helix	356-358	3
β-strand	366	1	36
β-strand	368-369	2	35
β-strand	377	1	37
β-strand	381-388	8	30

Chains G, H, I and J: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fibrin	A, D	protein	87	Homo sapiens	P02671 (AlphaFold model)
Fibrin	B, E	protein	328	Homo sapiens	P02675 (AlphaFold model)
Fibrin	C, F	protein	319	Homo sapiens	P02679 (AlphaFold model)
Fibrin	G, H	protein	4	Homo sapiens
Fibrin	I, J	protein	4	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>1FZC_1 FIBRIN (chains A, D)
VSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALA
REVDLKDYEDQQKQLEQVIAKDLLPSR

Sequence of entity 2 (B, E), FASTA

>1FZC_2 FIBRIN (chains B, E)
DNENVVNEYSSELEKHQLYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQMEYC
RTPCTVSCNIPVVSGKECEEIIRKGGETSEMYLIQPDSSVKPYRVYCDMNTENGGWTVIQ
NRQDGSVDFGRKWDPYKQGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIE
MEDWKGDKVKAHYGGFTVQNEANKYQISVNKYRGTAGNALMDGASQLMGENRTMTIHNGM
FFSTYDRDNDGWLTSDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGGQYTWDMAKHGTDD
GVVWMNWKGSWYSMRKMSMKIRPFFPQQ

Sequence of entity 3 (C, F), FASTA

>1FZC_3 FIBRIN (chains C, F)
KMLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHD
ITGKDCQDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKN
WIQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKV
GPEADKYRLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCA
EQDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKII
PFNRLTIGEGQQHHLGGAK

Sequence of entity 4 (G, H), FASTA

>1FZC_4 FIBRIN (chains G, H)
GPRP

Sequence of entity 5 (I, J), FASTA

>1FZC_5 FIBRIN (chains I, J)
GHRP

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CA	Calcium ion	Ca	4

Primary citation

Crystal structure of fragment double-D from human fibrin with two different bound ligands. Everse, S.J., Spraggon, G., Veerapandian, L. et al. Biochemistry (1998) 37:8637-8642. DOI 10.1021/bi9804129 · 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…
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…
3AT0 2.5 Å, Structural and biochemical characterization of ClfB:ligand interactions

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