SMTL ID : 3mvg.1

Native structure of IRIP, a type I ribosome inactivating protein from Iris hollandica var. at 1.25 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: S.29, P.40, Q.47, R.68 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.249 Salt bridges: A:R.68 SO4.11: 4 residues within 4Å: Chain B: L.84, A.90, P.99, R.101 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.101 SO4.12: 6 residues within 4Å: Chain A: F.241 Chain B: R.171, R.191, V.192, G.193, I.194 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.191, B:G.193, B:I.194 Water bridges: B:R.171 Salt bridges: B:R.171 SO4.13: 4 residues within 4Å: Chain B: R.81, H.100, P.141 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.81, B:H.100 SO4.14: 2 residues within 4Å: Chain B: P.61, H.137 3 PLIP interactions: 3 interactions with chain B Water bridges: B:P.61, B:N.80 Salt bridges: B:H.137

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: N.25, R.26, S.28, S.29, G.30, R.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.26, A:R.26, A:S.29, A:R.68 GOL.3: 2 residues within 4Å: Chain A: R.81, H.100 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.81, A:R.81, A:H.100 Water bridges: A:P.99, A:R.101 GOL.4: 2 residues within 4Å: Chain A: A.90, R.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.101, A:R.101 Water bridges: A:R.101 GOL.5: 5 residues within 4Å: Chain A: R.171, L.197, L.222, F.241 Chain B: F.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.171, A:R.171 GOL.6: 3 residues within 4Å: Chain A: S.107, Y.108 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.108 Water bridges: A:R.119 GOL.7: 3 residues within 4Å: Chain A: T.105, S.107, A.110 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.107 Water bridges: A:D.87, A:D.87, A:T.105, A:T.105 GOL.8: 4 residues within 4Å: Chain A: G.44, S.45, Q.46, N.91 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.46, A:Q.46, A:N.91 Water bridges: A:G.44, A:S.45 GOL.9: 5 residues within 4Å: Chain A: N.70, Y.72, S.107, R.164 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.70, A:R.164, A:R.164 GOL.10: 3 residues within 4Å: Chain A: T.12, R.14, S.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.12, A:R.14 Water bridges: A:T.12, A:S.15 GOL.15: 6 residues within 4Å: Chain B: H.100, T.103, P.142, T.143, E.145 Ligands: SO4.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.143, B:E.145 Water bridges: B:E.145 GOL.16: 4 residues within 4Å: Chain A: Q.228 Chain B: Q.227, Q.228, T.229 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.228, B:T.229, A:Q.228 GOL.17: 2 residues within 4Å: Chain B: S.107, Y.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.108 Water bridges: B:R.119, B:R.119 GOL.18: 4 residues within 4Å: Chain B: S.28, S.29, P.40, R.68 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.68, B:R.68 Water bridges: B:A.41, B:D.48 GOL.19: 5 residues within 4Å: Chain A: R.14 Chain B: T.12, R.14, S.15, D.18 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.12, B:R.14, B:D.18, A:R.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyer, A. et al., Native structure of IRIP, a type I ribosome inactivating protein from Iris hollandica var. at 1.25 A. to be published

Release Date

2011-06-01

Peptides

Ribosome inactivating type 1 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosome inactivating type 1 protein