SMTL ID : 6ig7.1

Crystal structure of thermolysin delivered in polyacrylamide using x-ray free electron laser

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.142, H.146, E.166 Ligands: LEU.6 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.2: 4 residues within 4Å: Chain A: Y.193, T.194, I.197, D.200 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.193, A:T.194, A:I.197, A:D.200, H2O.1 CA.3: 8 residues within 4Å: Chain A: D.138, E.177, D.185, E.187, I.188, G.189, E.190 Ligands: CA.5 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.4: 4 residues within 4Å: Chain A: D.57, D.59, Q.61, F.62 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.57, A:Q.61, H2O.1, H2O.3, H2O.5 CA.5: 7 residues within 4Å: Chain A: E.177, K.182, N.183, P.184, D.185, E.190 Ligands: CA.3 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.1, H2O.3

1 x LEU: LEUCINE(Non-covalent)

LEU.6: 15 residues within 4Å: Chain A: N.112, A.113, F.114, F.130, L.133, V.139, H.142, E.143, I.188, G.189, L.202, R.203, H.231 Ligands: ZN.1, LYS.7 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:L.133, A:V.139, A:L.202 Hydrogen bonds: A:N.112, A:R.203, A:R.203

1 x LYS: LYSINE(Non-covalent)

LYS.7: 7 residues within 4Å: Chain A: N.111, N.112, F.130, L.202, R.203, H.231 Ligands: LEU.6 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.202 Hydrogen bonds: A:N.111, A:N.112, A:N.112 Salt bridges: A:H.231, K.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., Polyacrylamide injection matrix for serial femtosecond crystallography. Sci Rep (2019)

Release Date

2018-11-07

Peptides

Thermolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermolysin

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