SMTL ID : 9csm.1

Crystal structure of human ribonuclease 7 (RNase 7, HsR7)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

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

CL.1: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: K.13, M.17, F.49 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: H.16, N.42, T.43, L.125 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: K.64, R.127, V.128 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: D.67 Ligands: ZN.12 Ligand excluded by PLIP CL.6: 7 residues within 4Å: Chain A: C.63, K.64, N.65, H.124, D.126 Ligands: CL.7, ZN.13 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: K.64, H.124, D.126 Ligands: CL.6, ZN.13 Ligand excluded by PLIP CL.8: 8 residues within 4Å: Chain A: W.11, F.12, Q.15, H.16, V.123, H.124 Ligands: CL.9, ZN.14 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: H.16, H.124, L.125 Ligands: CL.8, ZN.14 Ligand excluded by PLIP CL.10: 8 residues within 4Å: Chain A: M.6, I.14, K.33, H.34 Ligands: CL.11, ZN.15, PEG.21, MES.23 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: K.33, H.34 Ligands: CL.10, ZN.15 Ligand excluded by PLIP

4 x ZN: ZINC ION(Non-covalent)

ZN.12: 2 residues within 4Å: Chain A: D.67 Ligands: CL.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.67, A:D.67 ZN.13: 6 residues within 4Å: Chain A: C.63, K.64, H.124, D.126 Ligands: CL.6, CL.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.124, A:D.126 ZN.14: 6 residues within 4Å: Chain A: Q.15, H.16, H.124, L.125 Ligands: CL.8, CL.9 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.16, H2O.4 ZN.15: 4 residues within 4Å: Chain A: K.33, H.34 Ligands: CL.10, CL.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.34

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.16: 2 residues within 4Å: Chain A: K.95 Ligands: MPD.22 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.95 MES.23: 6 residues within 4Å: Chain A: M.6, Q.10, K.13, I.14 Ligands: CL.10, PEG.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.10, A:Q.10

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.17: 6 residues within 4Å: Chain A: K.36, R.37, C.38, G.87, K.88, H.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.37, A:C.38, A:H.89 EDO.19: 5 residues within 4Å: Chain A: E.47, A.76, V.77, S.78, N.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.78 EDO.20: 3 residues within 4Å: Chain A: K.39, D.40, L.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.40, A:L.41, A:L.41

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 5 residues within 4Å: Chain A: K.112, K.113, D.114, S.115, Q.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.113, A:Q.116 PEG.21: 6 residues within 4Å: Chain A: I.14, N.30, K.33, H.34 Ligands: CL.10, MES.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.33 Water bridges: A:N.30, A:N.30

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.22: 5 residues within 4Å: Chain A: K.95, E.96, K.97, R.98 Ligands: MES.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.95, A:E.96, A:E.96, A:R.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, T.T.Q. et al., Crystal structure of human ribonuclease 7 (RNase 7, HsR7). To Be Published

Release Date

2025-07-30

Peptides

Ribonuclease 7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease 7

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