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BMRB: 15120

2JNP

SOLUTION STRUCTURE OF MATRIX METALLOPROTEINASE 3 (MMP-3) IN THE PRESENCE OF N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID (NNGH)

Authors

Alcaraz, L.A., Banci, L., Bertini, I., Cantini, F., Donaire, A., Gonnelli, L.

Assembly

MMP3 complexed with NNGH

Entity

1. MMP3 (polymer, Thiol state: not present), 161 monomers, 18022.85 Da Detail

GIPKWRKTHL TYRIVNYTPD LPKDAVDSAV EKALKVWEEV TPLTFSRLYE GEADIMISFA VREHGDFYPF DGPGNVLAHA YAPGPGINGD AHFDDDEQWT KDTTGTNLFL VAAHEIGHSL GLFHSANTEA LMYPLYHSLT DLTRFRLSQD DINGIQSLYG P

2. ZN (non-polymer), 65.409 × 2 Da
3. CA (non-polymer), 40.078 × 2 Da
4. NGH (non-polymer), 316.373 Da

Total weight

18550.197 Da

Max. entity weight

18022.85 Da

Entity Connection

na 19 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:HIS114:HE2	2:ZN1:ZN
2	na	sing	1:HIS118:HE2	2:ZN1:ZN
3	na	sing	1:HIS124:HE2	2:ZN1:ZN
4	na	sing	4:NGH1:O2	2:ZN1:ZN
5	na	sing	4:NGH1:O3	2:ZN1:ZN
6	na	sing	1:HIS64:HE2	2:ZN1:ZN
7	na	sing	1:HIS79:HE2	2:ZN1:ZN
8	na	sing	1:HIS92:HE2	2:ZN1:ZN
9	na	sing	1:ASP66:OD1	2:ZN1:ZN
10	na	sing	1:GLY72:O	3:CA1:CA
11	na	sing	1:GLY74:O	3:CA1:CA
12	na	sing	1:VAL76:O	3:CA1:CA
13	na	sing	1:ASP71:OD1	3:CA1:CA
14	na	sing	1:ASP94:OD1	3:CA1:CA
15	na	sing	1:GLU97:OE2	3:CA1:CA
16	na	sing	1:ASP54:OD1	3:CA1:CA
17	na	sing	1:GLY86:O	3:CA1:CA
18	na	sing	1:ASN88:OD1	3:CA1:CA
19	na	sing	1:ASP90:OD1	3:CA1:CA

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 67.2 %, Completeness (bb): 74.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	67.2 % (1244 of 1850)	76.3 % (723 of 948)	49.3 % (364 of 739)	96.3 % (157 of 163)
Backbone	74.7 % (707 of 946)	94.2 % (306 of 325)	53.8 % (253 of 470)	98.0 % (148 of 151)
Sidechain	61.9 % (651 of 1052)	66.9 % (417 of 623)	54.0 % (225 of 417)	75.0 % (9 of 12)
Aromatic	17.5 % (37 of 212)	32.1 % (34 of 106)	0.0 % (0 of 103)	100.0 % (3 of 3)
Methyl	84.8 % (151 of 178)	96.6 % (86 of 89)	73.0 % (65 of 89)

1. MMP3

GIPKWRKTHL TYRIVNYTPD LPKDAVDSAV EKALKVWEEV TPLTFSRLYE GEADIMISFA VREHGDFYPF DGPGNVLAHA YAPGPGINGD AHFDDDEQWT KDTTGTNLFL VAAHEIGHSL GLFHSANTEA LMYPLYHSLT DLTRFRLSQD DINGIQSLYG P

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details Tris 20mM, pH 8, ZnCl2 0.1mM, CaCl2 5mM, NaCl 300mM

#	Name	Isotope labeling	Concentration
1	MMP3	natural abundance	1 mM
2	TRIS	natural abundance	20 mM
3	sodium chloride	natural abundance	300 mM
4	ZnCl2	natural abundance	0.1 mM
5	CaCl2	natural abundance	5 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details Tris 20mM, pH 8, ZnCl2 0.1mM, CaCl2 5mM, NaCl 300mM

#	Name	Isotope labeling	Concentration
6	MMP3	[U-98% 13C; U-98% 15N]	1 mM
7	TRIS	natural abundance	20 mM
8	sodium chloride	natural abundance	300 mM
9	ZnCl2	natural abundance	0.1 mM
10	CaCl2	natural abundance	5 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8, Details Tris 20mM, pH 8, ZnCl2 0.1mM, CaCl2 5mM, NaCl 300mM

#	Name	Isotope labeling	Concentration
11	MMP3	[U-99% 15N]	1 mM
12	TRIS	natural abundance	20 mM
13	sodium chloride	natural abundance	300 mM
14	ZnCl2	natural abundance	0.1 mM
15	CaCl2	natural abundance	5 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 2.66 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 2.66 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.09 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 25 models in PDB: 2JNP, Strand ID: A Detail

Release date

2007-10-16

Citation

Matrix metalloproteinase-inhibitor interaction: the solution structure of the catalytic domain of human matrix metalloproteinase-3 with different inhibitors
Alcaraz, L.A., Banci, L., Bertini, I., Cantini, F., Donaire, A., Gonnelli, L.
J. Biol. Inorg. Chem. (2007), 12, 1197-1206, PubMed 17710450 , DOI 10.1007/s00775-007-0288-9 , Abstract

Related entities 1. MMP3, : 1 : 37 : 1 : 7 : 232 entities Detail

Interaction partners 1. MMP3, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 12 experiments Detail

1 2D 1H-1H NOESY