1EAK: Catalytic domain of proMMP-2 E404Q mutant

Catalytic domain of proMMP-2 E404Q mutant. Determined by X-ray diffraction at 2.66 Å resolution. Released 22 Aug 2002.

Method: X-ray diffraction
Resolution: 2.66 Å
Organisms: HOMO SAPIENS, SYNTHETIC CONSTRUCT
Chains: 6
Atoms: 13,504
Mol. weight: 191.88 kDa
Ligands: ZN, CA
Released: 22 Aug 2002

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

Secondary structure: helices and β-sheets

1EAK contains 60 α-helices and 132 β-strands across 4 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: 17 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	35-37	3
α-helix	40-45	6
α-helix	46-53	8
α-helix	54-58	5
α-helix	67-80	14
α-helix	91-97	7
β-strand	101	1	1
β-strand	123-128	6	2
α-helix	137-152	16
β-strand	158-161	4	2
β-strand	169-174	6	2
β-strand	190	1	1
β-strand	192-194	3	2
α-helix	195-196	2
β-strand	205-208	4	2
β-strand	213-214	2	3
β-strand	222	1	4
β-strand	224	1	5
α-helix	226-228	3
β-strand	232	1	4
α-helix	233	1
β-strand	237-239	3	6
β-strand	242-244	3	6
β-strand	248	1	5
β-strand	258-260	3	5
β-strand	264	1	6
β-strand	271-273	3	5
α-helix	274-275	2
α-helix	289-291	3
β-strand	295-297	3	7
β-strand	300-302	3	7
β-strand	306	1	8
β-strand	316-318	3	8
β-strand	329-331	3	8
β-strand	340	1	9
β-strand	353-355	3	10
β-strand	358-360	3	10
β-strand	364	1	9
β-strand	374-376	3	9
α-helix	381-384	4
β-strand	387-389	3	9
α-helix	390-391	2
β-strand	395-396	2	3
α-helix	397-408	12
β-strand	424	1	1
α-helix	435-445	11
α-helix	447-449	3

Chain B: 16 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	40-45	6
α-helix	46-57	12
α-helix	67-80	14
α-helix	91-97	7
β-strand	101	1	11
β-strand	123-128	6	12
α-helix	137-152	16
β-strand	158-161	4	12
β-strand	169-174	6	12
β-strand	190	1	11
β-strand	192-194	3	12
α-helix	195-196	2
β-strand	205-208	4	12
β-strand	213-214	2	13
β-strand	222	1	14
β-strand	224	1	15
α-helix	231	1
β-strand	232	1	14
α-helix	233	1
β-strand	237-239	3	16
β-strand	242-244	3	16
β-strand	248	1	15
β-strand	258-260	3	15
β-strand	264	1	16
α-helix	265-268	4
β-strand	271-273	3	15
α-helix	274-275	2
β-strand	276	1	17
β-strand	280	1	17
β-strand	282	1	18
α-helix	289-291	3
β-strand	295-297	3	19
β-strand	300-302	3	19
β-strand	306	1	18
β-strand	316-318	3	18
β-strand	322	1	19
α-helix	323-326	4
β-strand	329-331	3	18
β-strand	340	1	20
β-strand	353-355	3	21
β-strand	358-360	3	21
β-strand	364	1	20
β-strand	374-376	3	20
β-strand	380	1	21
α-helix	381-384	4
β-strand	387-389	3	20
α-helix	390-391	2
β-strand	395-396	2	13
α-helix	397-408	12
β-strand	424	1	11
α-helix	435-445	11

Chain C: 13 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	40-43	4
α-helix	46-56	11
α-helix	68-80	13
α-helix	91-97	7
β-strand	101	1	22
β-strand	123-128	6	23
α-helix	137-152	16
β-strand	158-161	4	23
β-strand	169-174	6	23
β-strand	190	1	22
β-strand	192-194	3	23
β-strand	205-208	4	23
β-strand	213-214	2	24
β-strand	222	1	25
β-strand	224	1	26
α-helix	231	1
β-strand	232	1	25
α-helix	233	1
β-strand	237-238	2	27
β-strand	243-244	2	27
β-strand	248	1	26
β-strand	258-260	3	26
β-strand	264	1	27
β-strand	271-273	3	26
α-helix	274-275	2
β-strand	282	1	28
α-helix	289-291	3
β-strand	295-296	2	7
β-strand	301-302	2	7
β-strand	306	1	28
β-strand	316-318	3	28
β-strand	322	1	7
α-helix	323-326	4
β-strand	329-331	3	28
β-strand	340	1	29
β-strand	353-355	3	30
β-strand	358-360	3	30
β-strand	364	1	29
β-strand	374-376	3	29
β-strand	380	1	30
β-strand	387-389	3	29
α-helix	390-391	2
β-strand	395-396	2	24
α-helix	397-409	13
β-strand	424	1	22
α-helix	435-442	8

Chain D: 14 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	42-45	4
α-helix	46-57	12
α-helix	70-80	11
α-helix	91-97	7
β-strand	101	1	31
β-strand	123-128	6	32
α-helix	137-152	16
β-strand	158-161	4	32
β-strand	169-174	6	32
β-strand	190	1	31
β-strand	192-194	3	32
α-helix	195-196	2
β-strand	205-208	4	32
β-strand	213-214	2	33
β-strand	222	1	34
β-strand	224	1	35
α-helix	231	1
β-strand	232	1	34
α-helix	233	1
β-strand	237-238	2	36
β-strand	243-244	2	36
β-strand	248	1	35
β-strand	258-260	3	35
β-strand	264	1	36
β-strand	271-273	3	35
α-helix	274-275	2
β-strand	276	1	37
β-strand	280	1	37
β-strand	282	1	38
α-helix	289-291	3
β-strand	295-297	3	19
β-strand	300-302	3	19
β-strand	306	1	38
β-strand	316-318	3	38
β-strand	322	1	19
β-strand	329-331	3	38
β-strand	340	1	39
α-helix	347-349	3
β-strand	353-355	3	40
β-strand	358-360	3	40
β-strand	364	1	39
β-strand	374-376	3	39
β-strand	380	1	40
β-strand	387-389	3	39
α-helix	390-391	2
β-strand	395-396	2	33
α-helix	397-409	13
α-helix	435-444	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
72 kda type IV collagenase	A, B, C, D	protein	421	HOMO SAPIENS	P08253 (AlphaFold model)
Inhibitor peptide	P, R	protein	8	SYNTHETIC CONSTRUCT

Sequence of entity 1 (A, B, C, D), FASTA

>1EAK_1 72 KDA TYPE IV COLLAGENASE (chains A, B, C, D)
SPIIKFPGDVAPKTDKELAVQYLNTFYGCPKESCNLFVLKDTLKKMQKFFGLPQTGDLDQ
NTIETMRKPRCGNPDVANYNFFPRKPKWDKNQITYRIIGYTPDLDPETVDDAFARAFQVW
SDVTPLRFSRIHDGEADIMINFGRWEHGDGYPFDGKDGLLAHAFAPGTGVGGDSHFDDDE
LWTLGEGQVVRVKYGNADGEYCKFPFLFNGKEYNSCTDTGRSDGFLWCSTTYNFEKDGKY
GFCPHEALFTMGGNAEGQPCKFPFRFQGTSYDSCTTEGRTDGYRWCGTTEDYDRDKKYGF
CPETAMSTVGGNSEGAPCVFPFTFLGNKYESCTSAGRSDGKMWCATTANYDDDRKWGFCP
DQGYSLFLVAAHQFGHAMGLEHSQDPGALMAPIYTYTKNFRLSQDDIKGIQELYGASPDI
D

Sequence of entity 2 (P, R), FASTA

>1EAK_2 INHIBITOR PEPTIDE (chains P, R)
GPAGPPGA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
CA	Calcium ion	Ca	8

Water and common crystallization additives (SO4) are not listed.

Primary citation

Crystal Structure of Human Mmp-2 Reveals a New P. Bergmann, U., Tuuttila, A., Morgunova, E. et al. To be published.

Other PDB entries of the same protein (UniProt P08253 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3AYU 2.0 Å, Crystal structure of MMP-2 active site mutant in complex with APP-drived decapeptide…
7XJO 2.0 Å, Crystal structure of human MMP-2 catalytic domain in complex with inhibitor
1GEN 2.15 Å, C-terminal domain of gelatinase a
8H78 2.4 Å, Crystal structure of human MMP-2 catalytic domain in complex with inhibitor
1RTG 2.6 Å, C-terminal domain (haemopexin-like domain) of human matrix metalloproteinase-2
1CK7 2.8 Å, Gelatinase a (full-length)
1QIB 2.8 Å, Crystal structure of gelatinase a catalytic domain
7XGJ 2.8 Å, Crystal structure of human MMP-2 catalytic domain in complex with inhibitor
1GXD 3.1 Å, proMMP-2/TIMP-2 complex
1CXW The second type II module from human matrix metalloproteinase 2
1HOV Solution structure of a catalytic domain of mmp-2 complexed with sc-74020
1J7M The Third Fibronectin Type II Module from Human Matrix Metalloproteinase 2

Browse structure collections

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