SMTL ID : 3t8g.1

Thermolysin In Complex With UBTLN26

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x UBT: N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucylglycine(Non-covalent)

UBT.1: 18 residues within 4Å: Chain A: N.112, A.113, F.114, W.115, N.116, L.133, V.139, H.142, E.143, H.146, Y.157, E.166, L.202, R.203, H.231 Ligands: GOL.4, DMS.6, ZN.11 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.114, A:L.133, A:V.139, A:L.202 Hydrogen bonds: A:N.112, A:N.112, A:N.112, A:Y.157, A:R.203, A:R.203 Salt bridges: A:H.231

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: T.152, Q.273, Y.274, L.275, T.276 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.152 Water bridges: A:T.272, A:Y.274, A:L.275 GOL.3: 8 residues within 4Å: Chain A: Y.46, S.65, Y.66, A.68, P.69, H.105, D.124, P.132 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.65, A:D.124 GOL.4: 6 residues within 4Å: Chain A: F.114, W.115, E.143, H.146, Y.157 Ligands: UBT.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.115, A:E.143, A:N.165 Water bridges: A:D.150 GOL.5: 5 residues within 4Å: Chain A: G.109, Y.110, N.111, N.112 Ligands: DMS.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.109, A:N.111, A:N.111, A:N.112 Water bridges: A:N.111

5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 5 residues within 4Å: Chain A: Y.110, N.112, F.114 Ligands: UBT.1, GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.110 pi-Cation interactions: A:F.114 DMS.7: 5 residues within 4Å: Chain A: I.1, T.2, G.3, Q.31, N.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.3 DMS.8: 1 residues within 4Å: Chain A: Y.24 No protein-ligand interaction detected (PLIP) DMS.9: 3 residues within 4Å: Chain A: H.216, S.218, Y.251 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:H.216, A:Y.251 DMS.10: 1 residues within 4Å: Chain A: G.95 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 6 residues within 4Å: Chain A: H.142, H.146, Y.157, E.166, H.231 Ligands: UBT.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.142, A:H.146, A:E.166, A:E.166

4 x CA: CALCIUM ION(Non-covalent)

CA.12: 6 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, E.190 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.138, A:E.177, A:E.177, A:D.185, A:E.190 CA.13: 5 residues within 4Å: Chain A: E.177, N.183, D.185, E.190 Ligands: CA.12 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.177, A:N.183, A:D.185, A:E.190, H2O.16, H2O.16 CA.14: 4 residues within 4Å: Chain A: Y.193, T.194, I.197, D.200 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.193, A:I.197, A:D.200, H2O.16, H2O.16 CA.15: 3 residues within 4Å: Chain A: D.57, D.59, Q.61 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.57, A:Q.61, H2O.16, H2O.16, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biela, A. et al., Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding. Chemmedchem (2012)

Release Date

2012-08-01

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermolysin

Related Entries With Identical Sequence