1FZF: Fibrinogen

Crystal structure of fragment double-D from human fibrin with the peptide ligand gly-his-arg-pro-amide. Determined by X-ray diffraction at 2.7 Å resolution. Released 8 Jun 1999.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 10
Atoms: 10,581
Mol. weight: 170.87 kDa
Ligands: CA, NAG
Released: 8 Jun 1999

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

Secondary structure: helices and β-sheets

1FZF contains 51 α-helices and 111 β-strands across 7 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
α-helix	131-159	29
β-strand	165	1	1
α-helix	175-186	12

Chain B: 14 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	163-165	3
α-helix	169-192	24
β-strand	196	1	1
α-helix	197	1
β-strand	198-199	2	2
α-helix	202	1
β-strand	203-204	2	3
β-strand	207-208	2	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	272-274	3	4
β-strand	277-278	2	5
β-strand	288-289	2	5
β-strand	292-294	3	4
α-helix	296-303	8
β-strand	308-315	8	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
β-strand	376	1	6
β-strand	377	1	7
β-strand	380	1	7
α-helix	394-397	4
β-strand	402	1	6
β-strand	405	1	8
β-strand	407	1	8
β-strand	410-411	2	9
β-strand	415	1	10
β-strand	421	1	11
β-strand	434	1	10
β-strand	436-437	2	9
α-helix	438-441	4
β-strand	445	1	11
β-strand	449-456	8	4

Chain C: 10 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	104-134	31
α-helix	138-139	2
β-strand	140-141	2	2
β-strand	145	1	12
α-helix	153-158	6
β-strand	165-169	5	12
β-strand	178-184	7	12
β-strand	190-197	8	12
α-helix	208-213	6
β-strand	214-216	3	12
β-strand	217-218	2	3
β-strand	226-228	3	12
α-helix	230-237	8
β-strand	244-251	8	12
β-strand	257-263	7	12
β-strand	266-267	2	13
α-helix	270-272	3
β-strand	276-277	2	13
β-strand	280-283	4	12
β-strand	291	1	14
α-helix	303-305	3
β-strand	306	1	14
β-strand	310	1	13
α-helix	311-312	2
β-strand	313	1	15
β-strand	314	1	16
β-strand	317	1	16
α-helix	326-330	5
β-strand	334	1	15
β-strand	339	1	17
β-strand	342-343	2	18
β-strand	347	1	19
β-strand	353	1	20
β-strand	366	1	19
β-strand	368-369	2	18
β-strand	377	1	20
β-strand	381-388	8	12
α-helix	389-391	3

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	137-159	23
β-strand	165	1	21
α-helix	175-186	12

Chain E: 13 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	169-192	24
β-strand	196	1	21
α-helix	197	1
β-strand	198-199	2	22
α-helix	202	1
β-strand	203-204	2	23
β-strand	207-208	2	24
α-helix	211-216	6
β-strand	223-227	5	24
α-helix	234-235	2
β-strand	236-241	6	24
α-helix	244-246	3
β-strand	249-255	7	24
α-helix	266-271	6
β-strand	272-274	3	24
β-strand	277-278	2	25
β-strand	288-289	2	25
β-strand	292-294	3	24
α-helix	296-303	8
β-strand	309-315	7	24
β-strand	321-331	11	24
α-helix	334-336	3
β-strand	340-347	8	24
α-helix	352-355	4
α-helix	362-366	5
β-strand	376	1	26
β-strand	377	1	27
β-strand	380	1	27
α-helix	394-397	4
β-strand	402	1	26
β-strand	405	1	28
β-strand	407	1	28
β-strand	410-411	2	29
β-strand	415	1	30
β-strand	421	1	31
β-strand	434	1	30
β-strand	436-437	2	29
α-helix	438-441	4
β-strand	445	1	31
β-strand	449-455	7	24

Chain F: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	112-134	23
α-helix	138-139	2
β-strand	140-141	2	22
β-strand	145	1	32
α-helix	153-158	6
β-strand	165-169	5	32
β-strand	178-184	7	32
β-strand	190-197	8	32
α-helix	208-213	6
β-strand	214-216	3	32
β-strand	217-218	2	23
β-strand	226-228	3	32
α-helix	230-237	8
β-strand	244-251	8	32
β-strand	257-263	7	32
β-strand	266-267	2	33
α-helix	270-272	3
β-strand	276-277	2	33
β-strand	280-283	4	32
β-strand	291	1	34
α-helix	303-305	3
β-strand	306	1	34
α-helix	310-312	3
β-strand	313	1	35
β-strand	314	1	36
β-strand	317	1	36
α-helix	326-330	5
β-strand	334	1	35
β-strand	342-343	2	37
β-strand	347	1	38
β-strand	353	1	39
β-strand	366	1	38
β-strand	368-369	2	37
β-strand	377	1	39
β-strand	381-388	8	32
α-helix	389-391	3

Chain S: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fibrinogen	A, D	protein	87	Homo sapiens	P02671 (AlphaFold model)
Fibrinogen	B, E	protein	328	Homo sapiens	P02675 (AlphaFold model)
Fibrinogen	C, F	protein	319	Homo sapiens	P02679 (AlphaFold model)
Fibrinogen	M, N, S, T	protein	4	Homo sapiens	P02675 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>1FZF_1 FIBRINOGEN (chains A, D)
VSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALA
REVDLKDYEDQQKQLEQVIAKDLLPSR

Sequence of entity 2 (B, E), FASTA

>1FZF_2 FIBRINOGEN (chains B, E)
DNENVVNEYSSELEKHQLYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQMEYC
RTPCTVSCNIPVVSGKECEEIIRKGGETSEMYLIQPDSSVKPYRVYCDMNTENGGWTVIQ
NRQDGSVDFGRKWDPYKQGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIE
MEDWKGDKVKAHYGGFTVQNEANKYQISVNKYRGTAGNALMDGASQLMGENRTMTIHNGM
FFSTYDRDNDGWLTSDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGGQYTWDMAKHGTDD
GVVWMNWKGSWYSMRKMSMKIRPFFPQQ

Sequence of entity 3 (C, F), FASTA

>1FZF_3 FIBRINOGEN (chains C, F)
KMLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHD
ITGKDCQDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKN
WIQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKV
GPEADKYRLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCA
EQDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKII
PFNRLTIGEGQQHHLGGAK

Sequence of entity 4 (M, N, S, T), FASTA

>1FZF_4 FIBRINOGEN (chains M, N, S, T)
GHRP

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Conformational changes in fragments D and double-D from human fibrin(ogen) upon binding the peptide ligand Gly-His-Arg-Pro-amide. Everse, S.J., Spraggon, G., Veerapandian, L. et al. Biochemistry (1999) 38:2941-2946. DOI 10.1021/bi982626w · 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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