2E2D: Matrix metallopeptidase 13

Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2. Determined by X-ray diffraction at 2.0 Å resolution. Released 13 Mar 2007.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, Bos taurus
Chains: 2
Atoms: 3,052
Mol. weight: 39.01 kDa
Ligands: CA, ZN
Released: 13 Mar 2007

Explore 2E2D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2E2D contains 11 α-helices and 21 β-strands across 2 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: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	106	1	1
β-strand	117-122	6	2
α-helix	131-146	16
β-strand	152-155	4	2
β-strand	163-168	6	2
β-strand	184-188	5	2
β-strand	199-202	4	2
β-strand	207-208	2	3
β-strand	214-215	2	3
α-helix	216-227	12
β-strand	230	1	1
β-strand	243	1	2
α-helix	256-266	11

Chain C: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	1002-1003	2	2
α-helix	1008-1014	7
β-strand	1017-1033	17	4
β-strand	1039-1054	16	4
α-helix	1059-1060	2
β-strand	1062-1065	4	4
α-helix	1069-1071	3
β-strand	1083-1090	8	4
β-strand	1095-1097	3	4
β-strand	1104-1106	3	4
α-helix	1107-1109	3
α-helix	1112-1117	6
α-helix	1121-1125	5
β-strand	1129-1132	4	5
β-strand	1145-1148	4	5
α-helix	1150-1153	4
α-helix	1160-1164	5
β-strand	1166-1169	4	6
β-strand	1175-1178	4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Matrix metallopeptidase 13	A	protein	165	Homo sapiens	P45452 (AlphaFold model)
Metalloproteinase inhibitor 2	C	protein	180	Bos taurus	P16368 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2E2D_1 Matrix metallopeptidase 13 (chains A)
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADI
MISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHE
FGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGP

Sequence of entity 2 (C), FASTA

>2E2D_2 Metalloproteinase inhibitor 2 (chains C)
CSCSPVHPQQAFCNADIVIRAKAVNKKEVDSGNDIYGNPIKRIQYEIKQIKMFKGPDQDI
EFIYTAPAAAVCGVSLDIGGKKEYLIAGKAEGNGNMHITLCDFIVPWDTLSATQKKSLNH
RYQMGCECKITRCPMIPCYISSPDECLWMDWVTEKNINGHQAKFFACIKRSDGSCAWYRG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ZN	Zinc ion	Zn	2

Primary citation

Flexibility and Variability of TIMP Binding: X-ray Structure of the Complex Between Collagenase-3/MMP-13 and TIMP-2. Maskos, K., Lang, R., Tschesche, H. et al. J Mol Biol (2007) 366:1222-1231. DOI 10.1016/j.jmb.2006.11.072 · PubMed

Other PDB entries of the same protein (UniProt P45452 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5B5O 1.2 Å, Crystal structure of the catalytic domain of MMP-13 complexed with…
3ZXH 1.3 Å, MMP-13 complexed with 2-Napthylsulfonamide hydroxamic acid inhibitor
4JP4 1.43 Å, Mmp13 in complex with a reverse hydroxamate Zn-binder
3WV3 1.6 Å, Crystal structure of the catalytic domain of MMP-13 complexed with…
5B5P 1.6 Å, Crystal structure of the catalytic domain of MMP-13 complexed with…
5UWK 1.6 Å, Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-10a
830C 1.6 Å, Collagenase-3 (mmp-13) complexed to a sulphone-based hydroxamic acid
5UWM 1.62 Å, Matrix metalloproteinase-13 complexed with selective inhibitor compound (R)-17a
4L19 1.66 Å, Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1
1XUC 1.7 Å, Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor
2YIG 1.7 Å, MMP13 in complex with a novel selective non zinc binding inhibitor
6HV2 1.71 Å, MMP-13 in complex with the peptide IMISF

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