4P3D: MT1-MMP:Fab complex

MT1-MMP:Fab complex (Form II). Determined by X-ray diffraction at 1.95 Å resolution. Released 17 Dec 2014.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 7,895
Mol. weight: 98.99 kDa
Ligands: MG
Released: 17 Dec 2014

Explore 4P3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4P3D contains 33 α-helices and 94 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: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	3
β-strand	103-108	6	3
β-strand	112-114	3	3
β-strand	115-116	2	2
α-helix	120-121	2
β-strand	122	1	4
α-helix	123-124	2
β-strand	125-129	5	5
β-strand	140-150	11	5
β-strand	151	1	4
β-strand	156-159	4	6
α-helix	160-162	3
β-strand	164	1	6
β-strand	168-170	3	5
α-helix	171-173	3
β-strand	174-176	3	5
β-strand	179-189	11	5
α-helix	190-192	3
β-strand	199-204	6	6
α-helix	205-207	3
β-strand	209-214	6	6

Chain B: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	38-43	6	8
β-strand	49-54	6	8
β-strand	58-59	2	8
α-helix	60	1
β-strand	67-72	6	7
β-strand	75-80	6	7
α-helix	85-87	3
β-strand	89-95	7	8
α-helix	101	1
β-strand	102-103	2	8
β-strand	107-111	5	8
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	125-127	3
α-helix	128-131	4
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	150-156	7	11
β-strand	159-160	2	11
β-strand	165-170	6	10
β-strand	173	1	12
β-strand	176	1	12
β-strand	179-188	10	10
α-helix	189-194	6
β-strand	197-204	8	11
α-helix	210	1
β-strand	211-216	6	11

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	11-12	2	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	34-39	6	15
β-strand	45-51	7	15
β-strand	58-60	3	15
α-helix	62-64	3
β-strand	68-73	6	13
α-helix	74-76	3
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-100	9	15
β-strand	103-108	6	15
β-strand	112-114	3	15
β-strand	115-116	2	14
α-helix	119-121	3
β-strand	122	1	16
α-helix	123-124	2
β-strand	125-129	5	17
β-strand	140-150	11	17
β-strand	151	1	16
β-strand	156-159	4	18
α-helix	160-162	3
β-strand	164	1	18
β-strand	168-170	3	17
α-helix	171-173	3
β-strand	174-176	3	17
β-strand	179-189	11	17
α-helix	190-192	3
β-strand	199-204	6	18
α-helix	205-207	3
β-strand	209-214	6	18

Chain L: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-13	4	20
β-strand	19-25	7	19
β-strand	30	1	21
β-strand	36	1	21
β-strand	38-43	6	20
β-strand	49-54	6	20
β-strand	58-59	2	20
α-helix	60	1
β-strand	67-72	6	19
β-strand	75-80	6	19
α-helix	85-87	3
β-strand	89-95	7	20
α-helix	101	1
β-strand	102-103	2	20
β-strand	107-111	5	20
β-strand	117	1	22
β-strand	120-124	5	23
α-helix	125-127	3
α-helix	128-131	4
β-strand	135-145	11	23
β-strand	146	1	22
β-strand	150-156	7	24
β-strand	159-161	3	24
β-strand	165-170	6	23
β-strand	173	1	25
β-strand	176	1	25
β-strand	179-188	10	23
α-helix	189-192	4
β-strand	197-204	8	24
β-strand	211-216	6	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy Chain Fab fragment of antibody LEM-2/15	A, H	protein	218	Mus musculus
Light Chain Fab fragment of antibody LEM-2/15	B, L	protein	218	Mus musculus	A2NHM3 (AlphaFold model)
Matrix metalloproteinase-14	C, M	protein	13	Homo sapiens	P50281 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>4P3D_1 Heavy Chain Fab fragment of antibody LEM-2/15 (chains A, H)
EVKLVESGGGLVKPGGSLKLSCAASGFIFSNYAMSWVRQTPEKRLEWVATISGGGRNIYS
LDSVKGRFTFFRDNARNTLYLQMSSLRSEDTAMYFCSRENYGSSFTYWGQGTLVTVSSAK
TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Sequence of entity 2 (B, L), FASTA

>4P3D_2 Light Chain Fab fragment of antibody LEM-2/15 (chains B, L)
DVLMTQTPLSLPVGLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHAPYTFGGGTKLEIKRAADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 3 (C, M), FASTA

>4P3D_3 Matrix metalloproteinase-14 (chains C, M)
FDSAEPWTVRNED

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Water and common crystallization additives (EDO, EPE, GOL, CL) are not listed.

Primary citation

Inhibition mechanism of membrane metalloprotease by an exosite-swiveling conformational antibody. Udi, Y., Grossman, M., Solomonov, I. et al. Structure (2015) 23:104-115. DOI 10.1016/j.str.2014.10.012 · PubMed

Other PDB entries of the same protein (UniProt A2NHM3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PXR 1.56 Å, Anti-TAU BIIB092 FAB with TAU peptide
4TPR 1.6 Å, Structure of Tau5 antibody Fab fragment
4TQE 1.6 Å, Structure of tau peptide in complex with Tau5 antibody Fab fragment
3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
2IPU 1.65 Å, PFA1 Fab fragment complexed with Abeta 1-8 peptide
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
2DQU 1.7 Å, Crystal form II: high resolution crystal structure of the complex of the hydrolytic…
3UYR 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
1ZEA 1.78 Å, Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide
1PZ5 1.8 Å, Structural basis of peptide-carbohydrate mimicry in an antibody combining site
2DQT 1.8 Å, High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and…

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