- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x 8MC- PRO- LEU- GLY- PFF- DNW- ALA- ARG- NH2: fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2)(Non-covalent)
- 2 x AZI: AZIDE ION(Non-covalent)
AZI.3: 11 residues within 4Å:- Chain A: A.84, H.85, A.86, H.121, A.122, H.125, H.131
- Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, ZN.4
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:A.84
AZI.16: 11 residues within 4Å:- Chain B: A.84, H.85, A.86, H.121, A.122, H.125, H.131
- Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.2, 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.2, 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.2, ZN.17
No protein-ligand interaction detected (PLIP)- 4 x ZN: ZINC ION(Non-covalent)
ZN.4: 5 residues within 4Å:- Chain A: H.121, H.125, H.131
- Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, AZI.3
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:H.121, A:H.125, A:H.131
ZN.5: 4 residues within 4Å:- Chain A: H.70, D.72, H.85, H.98
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:H.70, A:D.72, A:H.85, A:H.98
ZN.17: 5 residues within 4Å:- Chain B: H.121, H.125, H.131
- Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.2, AZI.16
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:H.121, B:H.125, B:H.131
ZN.18: 4 residues within 4Å:- Chain B: H.70, D.72, H.85, H.98
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:H.70, B:D.72, B:H.85, B:H.98
- 3 x CA: CALCIUM ION(Non-covalent)
CA.6: 6 residues within 4Å:- Chain A: D.77, G.78, D.80, L.82, D.100, E.103
6 PLIP interactions:6 interactions with chain A- Metal complexes: A:D.77, A:G.78, A:D.80, A:L.82, A:D.100, A:E.103
CA.8: 4 residues within 4Å:- Chain A: D.26, D.101, E.103
- Ligands: PGO.15
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.26, A:D.101, A:E.103, H2O.8
CA.19: 6 residues within 4Å:- Chain B: D.77, G.78, D.80, L.82, D.100, E.103
6 PLIP interactions:6 interactions with chain B- Metal complexes: B:D.77, B:G.78, B:D.80, B:L.82, B:D.100, B:E.103
- 3 x SR: STRONTIUM ION(Non-functional Binders)
SR.7: 5 residues within 4Å:- Chain A: A.59, D.60, G.92, Q.94, D.96
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.60, A:G.92, A:Q.94, A:D.96, H2O.7
SR.20: 5 residues within 4Å:- Chain B: A.59, D.60, G.92, Q.94, D.96
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.60, B:G.92, B:Q.94, B:D.96, H2O.11
SR.21: 4 residues within 4Å:- Chain B: D.26, D.101, E.103
- Ligands: PGO.22
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.26, B:D.101, B:D.101, B:E.103, H2O.10
- 7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.9: 4 residues within 4Å:- Chain A: K.10, R.160, L.162, G.164
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.10
EDO.11: 6 residues within 4Å:- Chain A: Y.74, L.82, H.85
- Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.85
EDO.12: 7 residues within 4Å:- Chain A: A.137, L.138, M.142, Y.143, R.144, T.146
- Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:M.142, A:R.144
- Water bridges: A:E.136, A:R.144
EDO.13: 5 residues within 4Å:- Chain A: K.10, W.11, H.12, H.13
- Ligands: EDO.14
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:H.12, A:H.12, A:H.13
EDO.14: 4 residues within 4Å:- Chain A: H.13, G.90, P.91
- Ligands: EDO.13
No protein-ligand interaction detected (PLIP)EDO.23: 5 residues within 4Å:- Chain B: Y.74, L.82, H.85
- Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.2, 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.2
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:H.85
EDO.24: 3 residues within 4Å:- Chain B: L.9, G.128
- Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.2
2 PLIP interactions:2 interactions with chain B- Water bridges: B:H.125, B:L.129
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
PGO.15: 5 residues within 4Å:- Chain A: D.26, D.102, E.103, L.104
- Ligands: CA.8
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.26, A:L.104
PGO.22: 7 residues within 4Å:- Chain B: D.26, K.79, D.101, D.102, E.103, L.104
- Ligands: SR.21
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.26, B:D.101
- 3 x NA: SODIUM ION(Non-functional Binders)
NA.25: 5 residues within 4Å:- Chain A: L.42, P.149, P.150
- Chain B: P.149, P.150
No protein-ligand interaction detected (PLIP)NA.26: 3 residues within 4Å:- Chain B: A.137, L.138, R.144
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:A.137
- Water bridges: B:R.144
NA.27: 3 residues within 4Å:- Chain B: W.11, H.12, H.13
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:H.12, B:H.13
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Tranchant, I. et al., Halogen Bonding Controls Selectivity of FRET Substrate Probes for MMP-9. Chem.Biol. (2014)
- Release Date
- 2014-03-12
- Peptides
- Matrix metalloproteinase-9: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x 8MC- PRO- LEU- GLY- PFF- DNW- ALA- ARG- NH2: fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2)(Non-covalent)
- 2 x AZI: AZIDE ION(Non-covalent)
- 4 x ZN: ZINC ION(Non-covalent)
- 3 x CA: CALCIUM ION(Non-covalent)
- 3 x SR: STRONTIUM ION(Non-functional Binders)
- 7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
- 3 x NA: SODIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Tranchant, I. et al., Halogen Bonding Controls Selectivity of FRET Substrate Probes for MMP-9. Chem.Biol. (2014)
- Release Date
- 2014-03-12
- Peptides
- Matrix metalloproteinase-9: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B