SMTL ID : 8wfo.1

Durio zibethinus trypsin inhibitor DzTI-4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

3 x ACT: ACETATE ION

ACT.1: 8 residues within 4Å: Chain A: L.124, Q.125, F.142, P.144, T.152, L.153 Chain B: Y.101, W.108 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.101, B:W.108, A:L.124, A:Q.125 Hydrogen bonds: A:L.153 ACT.15: 4 residues within 4Å: Chain B: E.131, K.139, N.141, D.156 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.131 Water bridges: B:K.139, B:K.139 Salt bridges: B:K.139 ACT.16: 8 residues within 4Å: Chain A: Y.101, W.108 Chain B: L.124, Q.125, F.142, P.144, T.152, L.153 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.101, A:W.108, B:Q.125 Hydrogen bonds: B:T.152, B:L.153

18 x ZN: ZINC ION

ZN.2: 1 residues within 4Å: Chain A: D.113 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.113, H2O.5, H2O.8 ZN.3: 1 residues within 4Å: Chain A: K.97 No protein-ligand interaction detected (PLIP) ZN.4: 1 residues within 4Å: Chain A: D.99 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.99, H2O.1, H2O.5, H2O.7, H2O.8 ZN.5: 2 residues within 4Å: Chain A: D.102, S.104 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.102, A:S.104, H2O.2, H2O.6, H2O.6, H2O.7 ZN.6: 3 residues within 4Å: Chain A: D.11, E.12 Ligands: ZN.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.11, A:E.12, A:E.12 ZN.7: 3 residues within 4Å: Chain A: D.11, E.12 Ligands: ZN.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.12, H2O.2 ZN.8: 1 residues within 4Å: Chain A: E.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.3, H2O.3, H2O.6, H2O.7 ZN.9: 1 residues within 4Å: Chain A: N.2 No protein-ligand interaction detected (PLIP) ZN.10: 2 residues within 4Å: Chain A: H.162, D.163 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.162, H2O.5, H2O.8 ZN.11: 2 residues within 4Å: Chain A: K.1, D.66 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.66, H2O.7, H2O.8, H2O.9 ZN.14: 1 residues within 4Å: Chain B: D.11 No protein-ligand interaction detected (PLIP) ZN.17: 2 residues within 4Å: Chain B: H.162, D.163 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.162, B:D.163 ZN.18: 2 residues within 4Å: Chain B: D.102, S.104 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.102, B:S.104, H2O.9 ZN.19: 1 residues within 4Å: Chain B: D.99 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.99, H2O.10, H2O.13, H2O.14, H2O.16, H2O.17 ZN.20: 1 residues within 4Å: Chain B: E.12 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.12, H2O.12, H2O.15 ZN.21: 1 residues within 4Å: Chain B: D.40 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.40, B:D.40, H2O.10, H2O.16 ZN.22: 1 residues within 4Å: Chain B: D.55 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.55, H2O.10, H2O.17 ZN.23: 1 residues within 4Å: Chain B: D.66 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.66, H2O.14, H2O.16

3 x 1PE: PENTAETHYLENE GLYCOL

1PE.12: 6 residues within 4Å: Chain A: T.8, V.22, S.23, A.24, Y.56, K.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.56, A:K.180 1PE.13: 7 residues within 4Å: Chain A: A.28, K.107, W.109, R.159, Y.160, G.161, H.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.159, A:G.161 Water bridges: A:K.107, A:R.159 1PE.24: 4 residues within 4Å: Chain B: I.25, N.173, A.174, W.175 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deentanya, P. et al., Durio zibethinus trypsin inhibitor DzTI-4. To Be Published

Release Date

2024-09-25

Peptides

21 kDa seed protein-like: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

21 kDa seed protein-like

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