SMTL ID : 4hx2.1

Crystal structure of Streptomyces caespitosus sermetstatin in complex with Bacillus licheniformis subtilisin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-2-2-mer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: Q.2, D.41, L.74, N.76, T.78, V.80 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.41, A:D.41, A:L.74, A:T.78, A:V.80 CA.2: 5 residues within 4Å: Chain A: A.168, K.169, Y.170, D.171, V.173 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.168, A:Y.170, A:V.173, H2O.1, H2O.1 CA.13: 6 residues within 4Å: Chain C: Q.2, D.41, L.74, N.76, T.78, V.80 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.41, C:D.41, C:L.74, C:T.78, C:V.80 CA.14: 5 residues within 4Å: Chain C: A.168, K.169, Y.170, V.173, A.175 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.168, C:Y.170, C:V.173, H2O.9, H2O.11

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: H.237, Q.274 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.237, A:Q.274, H2O.3 ZN.9: 2 residues within 4Å: Chain B: H.4 Ligands: CAC.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.4, H2O.8

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: N.61, Y.208 Ligand excluded by PLIP

1 x 1AX: (2R,2'R)-3,3'-oxydipropane-1,2-diol(Non-covalent)

1AX.5: 9 residues within 4Å: Chain A: N.25, K.27, G.117, M.118, D.119, R.144, G.145, V.146 Ligands: PO4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.117, A:G.145

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 8 residues within 4Å: Chain A: D.119, G.145, P.238, N.239, L.240, S.241, A.242 Ligands: 1AX.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.238, A:A.242

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: R.185, Y.261, Y.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.185, A:Y.262 GOL.16: 3 residues within 4Å: Chain C: R.185, Y.261, Y.262 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.185, C:Y.262, C:Y.262

3 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.8: 6 residues within 4Å: Chain A: A.37, H.39, P.40, L.42, N.43, L.74 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.74 Hydrogen bonds: A:H.39 IPA.17: 4 residues within 4Å: Chain C: N.61, H.63, Y.208 Chain D: Y.73 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:H.63, C:Y.208 Hydrophobic interactions: D:Y.73 IPA.18: 4 residues within 4Å: Chain D: H.94, T.95, F.96, N.105 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.95, D:N.105

2 x K: POTASSIUM ION(Non-covalent)

K.10: 2 residues within 4Å: Chain B: H.94, N.105 No protein-ligand interaction detected (PLIP) K.11: 2 residues within 4Å: Chain B: K.93, H.94 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.94, H2O.7

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.12: 5 residues within 4Å: Chain B: A.3, H.4, N.86, R.88 Ligands: ZN.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.4

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.15: 5 residues within 4Å: Chain C: K.27, Y.90, W.112, N.116, M.118 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.90, C:W.112 Hydrogen bonds: C:Y.90 Salt bridges: C:K.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trillo-Muyo, S. et al., Mechanism of action of a Janus-faced single-domain protein inhibitor simultaneously targeting two peptidase classes. CHEM SCI (2013)

Release Date

2012-12-05

Peptides

KerA: AC
Neutral proteinase inhibitor ScNPI: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

KerA

Neutral proteinase inhibitor ScNPI

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