2Z4E: 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 2.7 Å resolution. Released 23 Oct 2007.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 10
Atoms: 10,646
Mol. weight: 172.13 kDa
Ligands: NAG, CA
Released: 23 Oct 2007

Explore 2Z4E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Z4E contains 51 α-helices and 108 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.

Chain A: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	130-159	30
β-strand	165	1	1
α-helix	175-189	15

Chain B: 12 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	168-192	25
β-strand	196	1	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	211-215	5
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	296-303	8
β-strand	308-315	8	4
β-strand	321-331	11	4
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
α-helix	394-398	5
β-strand	402	1	6
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: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	107-134	28
α-helix	139	1
β-strand	140-141	2	2
β-strand	145-150	6	12
α-helix	153-157	5
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	257-265	9	12
β-strand	266-267	2	13
α-helix	270-272	3
β-strand	276-277	2	13
β-strand	280-281	2	12
α-helix	289-291	3
α-helix	303-305	3
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
β-strand	366	1	18
β-strand	368-369	2	17
β-strand	377	1	19
β-strand	381-388	8	12
α-helix	389-391	3

Chain D: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	137-143	7
α-helix	145-159	15
β-strand	165	1	20
α-helix	175-187	13

Chain E: 11 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	170-192	23
β-strand	196	1	20
β-strand	198-199	2	21
α-helix	202	1
β-strand	203-204	2	22
β-strand	207-208	2	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	273-274	2	23
β-strand	277-278	2	24
β-strand	288-289	2	24
β-strand	292-293	2	23
α-helix	296-304	9
β-strand	308-315	8	23
β-strand	321-331	11	23
β-strand	340-347	8	23
α-helix	352-355	4
α-helix	362-366	5
β-strand	376	1	25
β-strand	377	1	26
β-strand	380	1	26
α-helix	394-398	5
β-strand	402	1	25
β-strand	407	1	27
β-strand	410-411	2	28
β-strand	415	1	29
β-strand	421	1	30
β-strand	434	1	29
β-strand	436-437	2	28
α-helix	438-441	4
β-strand	445	1	30
β-strand	449-456	8	23

Chain F: 12 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	116-133	18
α-helix	138-139	2
β-strand	140-141	2	21
β-strand	145-150	6	31
α-helix	153-157	5
β-strand	165-169	5	31
β-strand	178-184	7	31
β-strand	190-197	8	31
α-helix	208-213	6
β-strand	214-216	3	31
β-strand	217-218	2	22
β-strand	226-228	3	31
α-helix	230-237	8
β-strand	244-251	8	31
β-strand	257-265	9	31
β-strand	266-267	2	32
α-helix	270-272	3
β-strand	276-277	2	32
β-strand	280-283	4	31
α-helix	289-291	3
α-helix	303-305	3
α-helix	310-312	3
β-strand	313	1	33
β-strand	314	1	34
β-strand	317	1	34
α-helix	326-330	5
β-strand	334	1	33
β-strand	339	1	35
β-strand	342	1	36
β-strand	347	1	37
β-strand	353	1	38
α-helix	356-358	3
β-strand	366	1	37
β-strand	369	1	36
β-strand	377	1	38
β-strand	381-388	8	31
α-helix	389-391	3

Chains I, J, S and T: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fibrinogen alpha chain	A, D	protein	87	Homo sapiens	P02671 (AlphaFold model)
Fibrinogen beta chain	B, E	protein	326	Homo sapiens	P02675 (AlphaFold model)
Fibrinogen, gamma polypeptide	C, F	protein	324	Homo sapiens	P02679 (AlphaFold model)
Fibrin B knob (tetrapeptide)	S, T	protein	4
Fibrin B knob (pentapeptide)	I, J	protein	5		P02676 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>2Z4E_1 Fibrinogen alpha chain (chains A, D)
VSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALA
REVDLKDYEDQQKQLEQVIAKDLLPSR

Sequence of entity 2 (B, E), FASTA

>2Z4E_2 Fibrinogen beta chain (chains B, E)
DNENVVNEYSSELEKHQLYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQMEYC
RTPCTVSCNIPVVSGKECEEIIRKGGETSEMYLIQPDSSVKPYRVYCDMNTENGGWTVIQ
NRQDGSVDFGRKWDPYKQGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIE
MEDWKGDKVKAHYGGFTVQNEANKYQISVNKYRGTAGNALMDGASQLMGENRTMTIHNGM
FFSTYDRDNDGWLTSDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGGQYTWDMAKHGTDD
GVVWMNWKGSWYSMRKMSMKIRPFFP

Sequence of entity 3 (C, F), FASTA

>2Z4E_3 Fibrinogen, gamma polypeptide (chains C, F)
KMLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHD
ITGKDCQDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKN
WIQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKV
GPEADKYRLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCA
EQDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKII
PFNRLTIGEGQQHHLGGAKQAGDV

Sequence of entity 4 (S, T), FASTA

>2Z4E_4 Fibrin B knob (tetrapeptide) (chains S, T)
GHRP

Sequence of entity 5 (I, J), FASTA

>2Z4E_5 Fibrin B knob (pentapeptide) (chains I, J)
GHRPY

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CA	Calcium ion	Ca	8

Primary citation

Probing the beta-chain hole of fibrinogen with synthetic peptides that differ at their amino termini. Doolittle, R.F., Pandi, L. Biochemistry (2007) 46:10033-10038. DOI 10.1021/bi7010916 · 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…

Browse structure collections

About this viewer

MolViewer shows 2Z4E directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.