SMTL ID : 4dqw.1

Crystal Structure Analysis of PA3770

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-octamer

Ligands

16 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 19 residues within 4Å: Chain A: I.152, T.154, G.155, R.156, D.157, T.173, L.178, V.179, I.199, E.200, K.201 Chain B: R.156, R.198, E.200 Ligands: MN.2, ATP.3, MN.4, ATP.7, MN.8 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.154, A:G.155, A:R.156, A:D.157, A:T.173, A:V.179, A:V.179, A:E.200, B:R.198 Water bridges: A:R.159 Salt bridges: A:R.156, A:R.156, A:K.201, A:K.201, B:R.156, B:R.156, B:R.156 ATP.3: 14 residues within 4Å: Chain A: V.114, P.117, V.118, F.138, G.140, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: ATP.1, MN.2, MN.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.118, A:S.139, A:G.140, A:D.219, A:D.219 Salt bridges: A:K.201, A:K.201, A:R.218, A:R.218, A:R.218 pi-Stacking: A:F.138, A:F.138 ATP.7: 21 residues within 4Å: Chain A: R.156, R.198, E.200 Chain B: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201, L.203 Ligands: ATP.1, MN.4, MN.8, ATP.9, MN.10 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:R.198, B:R.156, B:D.157, B:V.179, B:V.179, B:E.200, B:E.200 Salt bridges: A:R.156, A:R.156, A:R.156, B:R.156, B:R.156, B:K.201, B:K.201 ATP.9: 16 residues within 4Å: Chain B: V.114, P.117, V.118, F.138, S.139, G.140, F.141, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: ATP.7, MN.8, MN.10 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.118, B:V.118, B:E.200, B:T.216, B:D.219 Salt bridges: B:K.201, B:K.201, B:R.218, B:R.218, B:R.218 Water bridges: A:R.159, A:R.159 ATP.11: 19 residues within 4Å: Chain C: I.152, T.154, G.155, R.156, D.157, T.173, L.178, V.179, I.199, E.200, K.201 Chain D: R.156, R.198, E.200 Ligands: MN.12, ATP.13, MN.14, ATP.17, MN.18 18 PLIP interactions: 13 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:T.154, C:G.155, C:R.156, C:D.157, C:T.173, C:V.179, C:V.179, C:E.200, D:R.198 Water bridges: C:R.159, D:E.200 Salt bridges: C:R.156, C:R.156, C:K.201, C:K.201, D:R.156, D:R.156, D:R.156 ATP.13: 14 residues within 4Å: Chain C: V.114, P.117, V.118, F.138, G.140, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: ATP.11, MN.12, MN.14 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:V.118, C:S.139, C:G.140, C:D.219, C:D.219 Salt bridges: C:K.201, C:K.201, C:R.218, C:R.218, C:R.218 pi-Stacking: C:F.138, C:F.138 ATP.17: 21 residues within 4Å: Chain C: R.156, R.198, E.200 Chain D: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201, L.203 Ligands: ATP.11, MN.14, MN.18, ATP.19, MN.20 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:R.156, D:D.157, D:V.179, D:V.179, D:E.200, D:E.200, C:R.198, C:E.200 Salt bridges: D:R.156, D:R.156, D:K.201, D:K.201, C:R.156, C:R.156, C:R.156 ATP.19: 16 residues within 4Å: Chain D: V.114, P.117, V.118, F.138, S.139, G.140, F.141, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: ATP.17, MN.18, MN.20 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:V.118, D:V.118, D:E.200, D:T.216, D:D.219 Salt bridges: D:K.201, D:K.201, D:R.218, D:R.218, D:R.218 Water bridges: C:R.159, C:R.159 ATP.21: 19 residues within 4Å: Chain E: I.152, T.154, G.155, R.156, D.157, T.173, L.178, V.179, I.199, E.200, K.201 Chain F: R.156, R.198, E.200 Ligands: MN.22, ATP.23, MN.24, ATP.27, MN.28 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:T.154, E:G.155, E:R.156, E:D.157, E:T.173, E:V.179, E:V.179, E:E.200, F:R.198 Water bridges: E:R.159 Salt bridges: E:R.156, E:R.156, E:K.201, E:K.201, F:R.156, F:R.156, F:R.156 ATP.23: 14 residues within 4Å: Chain E: V.114, P.117, V.118, F.138, G.140, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: ATP.21, MN.22, MN.24 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:V.118, E:S.139, E:G.140, E:D.219, E:D.219 Salt bridges: E:K.201, E:K.201, E:R.218, E:R.218, E:R.218 pi-Stacking: E:F.138, E:F.138 ATP.27: 21 residues within 4Å: Chain E: R.156, R.198, E.200 Chain F: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201, L.203 Ligands: ATP.21, MN.24, MN.28, ATP.29, MN.30 14 PLIP interactions: 4 interactions with chain E, 10 interactions with chain F Hydrogen bonds: E:R.198, F:R.156, F:D.157, F:V.179, F:V.179, F:E.200, F:E.200 Salt bridges: E:R.156, E:R.156, E:R.156, F:R.156, F:R.156, F:K.201, F:K.201 ATP.29: 16 residues within 4Å: Chain F: V.114, P.117, V.118, F.138, S.139, G.140, F.141, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: ATP.27, MN.28, MN.30 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:V.118, F:V.118, F:E.200, F:T.216, F:D.219 Salt bridges: F:K.201, F:K.201, F:R.218, F:R.218, F:R.218 Water bridges: E:R.159, E:R.159 ATP.31: 19 residues within 4Å: Chain G: I.152, T.154, G.155, R.156, D.157, T.173, L.178, V.179, I.199, E.200, K.201 Chain H: R.156, R.198, E.200 Ligands: MN.32, ATP.33, MN.34, ATP.37, MN.38 17 PLIP interactions: 13 interactions with chain G, 4 interactions with chain H Hydrogen bonds: G:T.154, G:G.155, G:R.156, G:D.157, G:T.173, G:V.179, G:V.179, G:E.200, H:R.198 Water bridges: G:R.159 Salt bridges: G:R.156, G:R.156, G:K.201, G:K.201, H:R.156, H:R.156, H:R.156 ATP.33: 14 residues within 4Å: Chain G: V.114, P.117, V.118, F.138, G.140, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: ATP.31, MN.32, MN.34 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:V.118, G:S.139, G:G.140, G:D.219, G:D.219 Salt bridges: G:K.201, G:K.201, G:R.218, G:R.218, G:R.218 pi-Stacking: G:F.138, G:F.138 ATP.37: 21 residues within 4Å: Chain G: R.156, R.198, E.200 Chain H: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201, L.203 Ligands: ATP.31, MN.34, MN.38, ATP.39, MN.40 14 PLIP interactions: 10 interactions with chain H, 4 interactions with chain G Hydrogen bonds: H:R.156, H:D.157, H:V.179, H:V.179, H:E.200, H:E.200, G:R.198 Salt bridges: H:R.156, H:R.156, H:K.201, H:K.201, G:R.156, G:R.156, G:R.156 ATP.39: 16 residues within 4Å: Chain H: V.114, P.117, V.118, F.138, S.139, G.140, F.141, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: ATP.37, MN.38, MN.40 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:V.118, H:V.118, H:E.200, H:T.216, H:D.219 Salt bridges: H:K.201, H:K.201, H:R.218, H:R.218, H:R.218 Water bridges: G:R.159, G:R.159

16 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: E.200 Ligands: ATP.1, ATP.3, MN.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.200 MN.4: 5 residues within 4Å: Chain A: E.200 Ligands: ATP.1, MN.2, ATP.3, ATP.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.200, H2O.8 MN.8: 5 residues within 4Å: Chain B: E.200 Ligands: ATP.1, ATP.7, ATP.9, MN.10 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.200, H2O.6 MN.10: 5 residues within 4Å: Chain B: E.200, K.201 Ligands: ATP.7, MN.8, ATP.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.200 MN.12: 4 residues within 4Å: Chain C: E.200 Ligands: ATP.11, ATP.13, MN.14 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.200 MN.14: 5 residues within 4Å: Chain C: E.200 Ligands: ATP.11, MN.12, ATP.13, ATP.17 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.200, H2O.16 MN.18: 5 residues within 4Å: Chain D: E.200 Ligands: ATP.11, ATP.17, ATP.19, MN.20 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.200, H2O.14 MN.20: 5 residues within 4Å: Chain D: E.200, K.201 Ligands: ATP.17, MN.18, ATP.19 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.200 MN.22: 4 residues within 4Å: Chain E: E.200 Ligands: ATP.21, ATP.23, MN.24 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.200 MN.24: 5 residues within 4Å: Chain E: E.200 Ligands: ATP.21, MN.22, ATP.23, ATP.27 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.200, H2O.24 MN.28: 5 residues within 4Å: Chain F: E.200 Ligands: ATP.21, ATP.27, ATP.29, MN.30 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.200, H2O.22 MN.30: 5 residues within 4Å: Chain F: E.200, K.201 Ligands: ATP.27, MN.28, ATP.29 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.200 MN.32: 4 residues within 4Å: Chain G: E.200 Ligands: ATP.31, ATP.33, MN.34 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.200 MN.34: 5 residues within 4Å: Chain G: E.200 Ligands: ATP.31, MN.32, ATP.33, ATP.37 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.200, H2O.32 MN.38: 5 residues within 4Å: Chain H: E.200 Ligands: ATP.31, ATP.37, ATP.39, MN.40 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.200, H2O.30 MN.40: 5 residues within 4Å: Chain H: E.200, K.201 Ligands: ATP.37, MN.38, ATP.39 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.200

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 4 residues within 4Å: Chain A: G.358, G.359, G.380, S.381 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.359, A:G.380, A:S.381, A:S.381 PO4.15: 4 residues within 4Å: Chain C: G.358, G.359, G.380, S.381 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.359, C:G.380, C:S.381, C:S.381 PO4.25: 4 residues within 4Å: Chain E: G.358, G.359, G.380, S.381 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.359, E:G.380, E:S.381, E:S.381 PO4.35: 4 residues within 4Å: Chain G: G.358, G.359, G.380, S.381 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:G.359, G:G.380, G:S.381, G:S.381

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: H.109, T.111, K.222, A.223, Y.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.222, A:K.222 GOL.16: 5 residues within 4Å: Chain C: H.109, T.111, K.222, A.223, Y.226 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.222, C:K.222 GOL.26: 5 residues within 4Å: Chain E: H.109, T.111, K.222, A.223, Y.226 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.222, E:K.222 GOL.36: 5 residues within 4Å: Chain G: H.109, T.111, K.222, A.223, Y.226 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:K.222, G:K.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Labesse, G. et al., MgATP Regulates Allostery and Fiber Formation in IMPDHs. Structure (2013)

Release Date

2013-03-06

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Inosine-5'-monophosphate dehydrogenase

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