SMTL ID : 2zpo.2 (1 other biounit)

Crystal Structure of Green Turtle Egg White Ribonuclease

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: Q.10, H.11, K.41, V.113, H.114, Y.115 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.10, A:Y.115, A:Y.115 Salt bridges: A:H.11, A:K.41, A:H.114 SO4.2: 5 residues within 4Å: Chain A: R.117, A.118 Chain B: G.85, G.86, S.87 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.118, B:G.86, B:S.87 Water bridges: A:Q.101, A:Q.101, A:Y.115, A:R.117, B:Q.84, B:G.85 SO4.3: 5 residues within 4Å: Chain A: T.22, G.96, G.97, T.98 Ligands: GOL.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.98, A:T.98 SO4.4: 2 residues within 4Å: Chain A: T.2, R.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.3 Water bridges: A:Y.4 Salt bridges: A:R.3 SO4.5: 3 residues within 4Å: Chain A: R.82 Chain B: R.82 Ligands: SO4.17 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:R.82, A:N.95 Salt bridges: B:R.82, A:R.82 SO4.13: 6 residues within 4Å: Chain B: Q.10, H.11, K.41, V.113, H.114, Y.115 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.10, B:Y.115, B:Y.115 Salt bridges: B:H.11, B:K.41, B:H.114 SO4.14: 5 residues within 4Å: Chain A: G.85, G.86, S.87 Chain B: R.117, A.118 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.86, A:S.87, B:A.118 Water bridges: A:Q.84, A:G.85, B:T.45, B:Q.101, B:Q.101, B:R.117 SO4.15: 5 residues within 4Å: Chain B: T.22, G.96, G.97, T.98 Ligands: GOL.24 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.22, B:T.98, B:T.98 Water bridges: B:T.98, B:T.98 SO4.16: 2 residues within 4Å: Chain B: T.2, R.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.3 Water bridges: B:Y.4 Salt bridges: B:R.3 SO4.17: 3 residues within 4Å: Chain A: R.82 Chain B: R.82 Ligands: SO4.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.82, B:N.95 Salt bridges: B:R.82, A:R.82

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: D.71, R.102, I.119 Ligands: GOL.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.71, A:D.71, A:R.102, A:R.102 Water bridges: A:R.104, A:R.104 GOL.7: 4 residues within 4Å: Chain A: V.12, D.13, Y.14, R.33 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.13, A:D.13, A:Y.14, A:Y.14, A:R.33 Water bridges: A:R.33 GOL.8: 2 residues within 4Å: Chain A: G.67 Chain B: R.89 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.89, B:R.89, A:G.67 Water bridges: A:N.68 GOL.9: 4 residues within 4Å: Chain A: G.59, P.60, P.64, R.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.70, A:R.70 GOL.10: 3 residues within 4Å: Chain A: R.104, R.117 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.104 Water bridges: A:R.104 GOL.11: 4 residues within 4Å: Chain A: T.2, Y.4, E.5, L.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.5, A:E.5 GOL.12: 5 residues within 4Å: Chain A: D.21, T.22, R.23, G.96 Ligands: SO4.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.21, A:D.21, A:T.22, A:T.22, A:R.23, A:G.96 GOL.18: 4 residues within 4Å: Chain B: D.71, R.102, I.119 Ligands: GOL.22 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.71, B:R.102, B:R.102 Water bridges: B:R.104, B:R.104 GOL.19: 4 residues within 4Å: Chain B: V.12, D.13, Y.14, R.33 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.13, B:Y.14, B:Y.14, B:R.33 Water bridges: B:R.33 GOL.20: 2 residues within 4Å: Chain A: R.89 Chain B: G.67 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.89, A:R.89, B:G.67 Water bridges: B:N.68 GOL.21: 4 residues within 4Å: Chain B: G.59, P.60, P.64, R.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.70, B:R.70 GOL.22: 3 residues within 4Å: Chain B: R.104, R.117 Ligands: GOL.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.104 Water bridges: B:R.104 GOL.23: 4 residues within 4Å: Chain B: T.2, Y.4, E.5, L.111 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.2, B:E.5, B:E.5 GOL.24: 5 residues within 4Å: Chain B: D.21, T.22, R.23, G.96 Ligands: SO4.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.21, B:T.22, B:R.23, B:G.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katekaew, S. et al., Crystal Structure of Newly Found Green Turtle Egg White Ribonuclease. To be Published

Release Date

2008-08-19

Peptides

Ribonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ribonuclease

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