SMTL ID : 1yb5.2 (1 other biounit)

Crystal structure of human Zeta-Crystallin with bound NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: R.279, M.282 Chain B: V.72, Y.75, Y.81 Ligands: NAP.12 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.72, B:Y.75 Hydrogen bonds: B:Y.81 Water bridges: B:Y.75, A:R.279 Salt bridges: A:R.279 ACT.2: 3 residues within 4Å: Chain A: V.102, G.103, D.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.104, A:D.104 ACT.9: 6 residues within 4Å: Chain A: V.72, Y.75, Y.81 Chain B: R.279, M.282 Ligands: NAP.5 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:R.279 Salt bridges: B:R.279 Hydrophobic interactions: A:V.72, A:Y.75 Hydrogen bonds: A:Y.81 ACT.14: 6 residues within 4Å: Chain C: R.279, M.282 Chain D: V.72, Y.75, Y.81 Ligands: NAP.25 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Water bridges: C:R.279, D:Y.75 Salt bridges: C:R.279 Hydrophobic interactions: D:V.72, D:Y.75 Hydrogen bonds: D:Y.81 ACT.15: 3 residues within 4Å: Chain C: V.102, G.103, D.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.104, C:D.104 ACT.22: 6 residues within 4Å: Chain C: V.72, Y.75, Y.81 Chain D: R.279, M.282 Ligands: NAP.18 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.72, C:Y.75 Hydrogen bonds: C:Y.81 Water bridges: D:R.279 Salt bridges: D:R.279

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

CL.3: 6 residues within 4Å: Chain A: G.178, G.181, G.182, V.183, G.184 Ligands: NAP.5 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: S.119, T.120, I.121, A.131, A.132, T.135 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: G.178, G.181, G.182, V.183, G.184 Ligands: NAP.12 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: E.73, I.76, Y.89, P.91, G.92 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain C: G.178, G.181, G.182, V.183, G.184 Ligands: NAP.18 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain C: S.119, T.120, I.121, A.131, A.132, T.135 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain D: G.178, G.181, G.182, V.183, G.184 Ligands: NAP.25 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain D: E.73, I.76, Y.89, P.91, G.92 Ligand excluded by PLIP

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.5: 30 residues within 4Å: Chain A: P.71, Y.75, I.153, T.157, H.177, G.178, A.179, S.180, G.181, G.182, V.183, A.202, G.203, H.222, R.223, M.246, L.247, N.251, V.268, G.269, R.271, V.291, T.292, L.293, I.337, G.342, A.343 Chain B: M.282 Ligands: CL.3, ACT.9 33 PLIP interactions: 32 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.153, A:T.157, A:V.183 Hydrogen bonds: A:Y.75, A:Y.75, A:S.180, A:S.180, A:S.180, A:G.181, A:G.182, A:V.183, A:G.184, A:G.203, A:R.223, A:M.246, A:N.251, A:V.268, A:R.271, A:L.293, A:A.343 Water bridges: A:N.70, A:V.72, A:T.204, A:H.222, A:H.222, A:N.251, A:S.270, A:F.294, A:G.345, B:R.279 Salt bridges: A:H.222 pi-Stacking: A:H.222, A:H.222 NAP.12: 30 residues within 4Å: Chain A: M.282 Chain B: P.71, Y.75, I.153, T.157, H.177, G.178, A.179, S.180, G.181, G.182, V.183, A.202, G.203, H.222, R.223, M.246, L.247, N.251, V.268, G.269, R.271, V.291, T.292, L.293, I.337, G.342, A.343 Ligands: ACT.1, CL.10 32 PLIP interactions: 31 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.153, B:T.157, B:V.183 Hydrogen bonds: B:Y.75, B:Y.75, B:S.180, B:S.180, B:S.180, B:G.181, B:G.182, B:V.183, B:G.184, B:G.203, B:R.223, B:M.246, B:N.251, B:V.268, B:R.271, B:L.293, B:A.343 Water bridges: B:N.70, B:V.72, B:T.204, B:H.222, B:H.222, B:N.251, B:S.270, B:G.345, A:R.279 Salt bridges: B:H.222 pi-Stacking: B:H.222, B:H.222 NAP.18: 30 residues within 4Å: Chain C: P.71, Y.75, I.153, T.157, H.177, G.178, A.179, S.180, G.181, G.182, V.183, A.202, G.203, H.222, R.223, M.246, L.247, N.251, V.268, G.269, R.271, V.291, T.292, L.293, I.337, G.342, A.343 Chain D: M.282 Ligands: CL.16, ACT.22 33 PLIP interactions: 32 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.153, C:T.157, C:V.183 Hydrogen bonds: C:Y.75, C:Y.75, C:S.180, C:S.180, C:S.180, C:G.181, C:G.182, C:V.183, C:G.184, C:G.203, C:R.223, C:M.246, C:N.251, C:V.268, C:R.271, C:L.293, C:A.343 Water bridges: C:N.70, C:V.72, C:T.204, C:H.222, C:H.222, C:N.251, C:S.270, C:F.294, C:G.345, D:R.279 Salt bridges: C:H.222 pi-Stacking: C:H.222, C:H.222 NAP.25: 30 residues within 4Å: Chain C: M.282 Chain D: P.71, Y.75, I.153, T.157, H.177, G.178, A.179, S.180, G.181, G.182, V.183, A.202, G.203, H.222, R.223, M.246, L.247, N.251, V.268, G.269, R.271, V.291, T.292, L.293, I.337, G.342, A.343 Ligands: ACT.14, CL.23 32 PLIP interactions: 31 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.153, D:T.157, D:V.183 Hydrogen bonds: D:Y.75, D:Y.75, D:S.180, D:S.180, D:S.180, D:G.181, D:G.182, D:V.183, D:G.184, D:G.203, D:R.223, D:M.246, D:N.251, D:V.268, D:R.271, D:L.293, D:A.343 Water bridges: D:N.70, D:V.72, D:T.204, D:H.222, D:H.222, D:N.251, D:S.270, D:G.345, C:R.279 Salt bridges: D:H.222 pi-Stacking: D:H.222, D:H.222

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: A.193, Y.194, I.314, W.316 Chain D: A.193, Y.194, I.314, W.316 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:W.316, A:Y.194, A:Y.194 Water bridges: D:A.193 GOL.7: 3 residues within 4Å: Chain A: D.104, N.105, S.107 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.104, A:A.106, A:A.106, A:S.107 GOL.8: 7 residues within 4Å: Chain A: S.323, Y.325, N.336, G.340, S.341, G.342, M.347 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.323, A:Y.325, A:S.341, A:S.341 Water bridges: A:S.323 GOL.13: 7 residues within 4Å: Chain B: S.323, Y.325, N.336, G.340, S.341, G.342, M.347 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.323, B:Y.325, B:Y.325, B:S.341, B:S.341 Water bridges: B:S.323, B:G.340, B:T.344 GOL.19: 8 residues within 4Å: Chain B: A.193, Y.194, I.314, W.316 Chain C: A.193, Y.194, I.314, W.316 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:W.316, C:Y.194, C:Y.194 Water bridges: B:A.193 GOL.20: 3 residues within 4Å: Chain C: D.104, N.105, S.107 4 PLIP interactions: 4 interactions with chain C Water bridges: C:D.104, C:A.106, C:A.106, C:S.107 GOL.21: 7 residues within 4Å: Chain C: S.323, Y.325, N.336, G.340, S.341, G.342, M.347 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.323, C:Y.325, C:S.341, C:S.341 Water bridges: C:S.323 GOL.26: 7 residues within 4Å: Chain D: S.323, Y.325, N.336, G.340, S.341, G.342, M.347 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.323, D:Y.325, D:Y.325, D:S.341, D:S.341 Water bridges: D:S.323, D:G.340, D:T.344

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Debreczeni, J. et al., Crystal Structure of human Zeta-Crystallin at 1.85A. To be Published

Release Date

2004-12-28

Peptides

Quinone oxidoreductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Quinone oxidoreductase

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