SMTL ID : 8zei.1

Crystal structure of human cytosolic beta-alanyl lysine dipeptidase with crystal soaked in beta-alanyl histidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.142, H.144, E.183, H.395 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.142, A:E.183, A:H.395, H2O.2 ZN.2: 6 residues within 4Å: Chain A: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.142, A:H.144, A:H.207, H2O.1, H2O.2 ZN.8: 5 residues within 4Å: Chain B: C.142, H.144, E.183, H.395 Ligands: ZN.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.142, B:E.183, B:H.395, H2O.6 ZN.9: 6 residues within 4Å: Chain B: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.142, B:H.144, B:H.207, H2O.4, H2O.6 ZN.15: 5 residues within 4Å: Chain C: C.142, H.144, E.183, H.395 Ligands: ZN.16 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.142, C:E.183, C:H.395, H2O.9 ZN.16: 6 residues within 4Å: Chain C: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.15 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:C.142, C:H.144, C:H.207, H2O.8, H2O.9 ZN.22: 5 residues within 4Å: Chain D: C.142, H.144, E.183, H.395 Ligands: ZN.23 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.142, D:E.183, D:H.395, H2O.13 ZN.23: 6 residues within 4Å: Chain D: C.142, H.144, E.182, E.183, H.207 Ligands: ZN.22 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:C.142, D:H.144, D:H.207, H2O.11, H2O.13

4 x HIS: HISTIDINE(Non-covalent)

HIS.3: 9 residues within 4Å: Chain A: E.182, E.183, D.184, E.221, R.294, Y.332, S.367, S.369 Chain B: N.281 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.182, A:E.221, A:R.294, B:N.281 Salt bridges: H.3 HIS.10: 9 residues within 4Å: Chain A: N.281 Chain B: E.182, E.183, D.184, E.221, R.294, Y.332, S.367, S.369 6 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:E.182, B:E.221, B:R.294, B:Y.332, A:N.281 Salt bridges: H.10 HIS.17: 9 residues within 4Å: Chain C: E.182, E.183, D.184, E.221, R.294, Y.332, S.367, S.369 Chain D: N.281 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: C:E.182, C:E.221, C:R.294, D:N.281 Salt bridges: H.17 HIS.24: 9 residues within 4Å: Chain C: N.281 Chain D: E.182, E.183, D.184, E.221, R.294, Y.332, S.367, S.369 6 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: C:N.281, D:E.182, D:E.221, D:R.294, D:Y.332 Salt bridges: H.24

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 1 residues within 4Å: Chain A: E.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.47 TRS.11: 1 residues within 4Å: Chain B: E.47 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.47 TRS.18: 1 residues within 4Å: Chain C: E.47 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.47 TRS.25: 1 residues within 4Å: Chain D: E.47 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.47

8 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 2 residues within 4Å: Chain A: Y.71, L.101 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.71 ACY.6: 7 residues within 4Å: Chain A: P.239, P.280, N.281, I.282, I.283 Chain B: H.270, Y.292 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.239, A:I.283 Salt bridges: B:H.270 ACY.12: 2 residues within 4Å: Chain B: Y.71, L.101 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.71 ACY.13: 7 residues within 4Å: Chain A: H.270, Y.292 Chain B: P.239, P.280, N.281, I.282, I.283 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.239, B:I.283 Hydrogen bonds: A:Y.292 Salt bridges: A:H.270 ACY.19: 2 residues within 4Å: Chain C: Y.71, L.101 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.71 ACY.20: 7 residues within 4Å: Chain C: P.239, P.280, N.281, I.282, I.283 Chain D: H.270, Y.292 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:P.239, C:I.283 Salt bridges: D:H.270 ACY.26: 2 residues within 4Å: Chain D: Y.71, L.101 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.71 ACY.27: 7 residues within 4Å: Chain C: H.270, Y.292 Chain D: P.239, P.280, N.281, I.282, I.283 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:P.239, D:I.283 Hydrogen bonds: C:Y.292 Salt bridges: C:H.270

4 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain A: E.51, E.54, R.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.55, A:R.55 NA.14: 3 residues within 4Å: Chain B: E.51, E.54, R.55 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.55, B:R.55 NA.21: 3 residues within 4Å: Chain C: E.51, E.54, R.55 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.51, C:R.55, C:R.55 NA.28: 3 residues within 4Å: Chain D: E.51, E.54, R.55 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.51, D:R.55, D:R.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandravanshi, K. et al., Crystal structure of human cytosolic beta-alanyl lysine dipeptidase with crystal soaked in beta-alanyl histidine. To Be Published

Release Date

2025-05-14

Peptides

Xaa-Arg dipeptidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Xaa-Arg dipeptidase

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