SMTL ID : 4qne.1

Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with NAD and IMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-octamer

Ligands

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 23 residues within 4Å: Chain A: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, V.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.294, G.295 Ligands: NAJ.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.156, A:S.182, A:D.217, A:G.219, A:G.240, A:S.241, A:M.267, A:G.268, A:E.294 Water bridges: A:K.175, A:G.179, A:G.181, A:I.220, A:I.220, A:M.242 IMP.4: 23 residues within 4Å: Chain B: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, V.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.294, G.295 Ligands: NAJ.5 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.156, B:S.182, B:D.217, B:G.219, B:G.240, B:S.241, B:S.241, B:Y.264, B:M.267, B:G.268, B:E.294 Water bridges: B:G.179, B:G.181, B:I.220, B:I.220, B:I.220, B:S.241, B:S.241, B:M.242 IMP.7: 23 residues within 4Å: Chain C: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, V.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.294, G.295 Ligands: NAJ.8 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:N.156, C:S.182, C:D.217, C:G.219, C:G.240, C:S.241, C:M.267, C:G.268, C:E.294 Water bridges: C:K.175, C:G.179, C:G.181, C:I.220, C:I.220, C:M.242 IMP.10: 23 residues within 4Å: Chain D: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, V.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.294, G.295 Ligands: NAJ.11 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:N.156, D:S.182, D:D.217, D:G.219, D:G.240, D:S.241, D:S.241, D:Y.264, D:M.267, D:G.268, D:E.294 Water bridges: D:G.179, D:G.181, D:I.220, D:I.220, D:I.220, D:S.241, D:S.241, D:M.242 IMP.13: 23 residues within 4Å: Chain E: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, V.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.294, G.295 Ligands: NAJ.14 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:N.156, E:S.182, E:D.217, E:G.219, E:G.240, E:S.241, E:M.267, E:G.268, E:E.294 Water bridges: E:K.175, E:G.179, E:G.181, E:I.220, E:I.220, E:M.242 IMP.16: 23 residues within 4Å: Chain F: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, V.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.294, G.295 Ligands: NAJ.17 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:N.156, F:S.182, F:D.217, F:G.219, F:G.240, F:S.241, F:S.241, F:Y.264, F:M.267, F:G.268, F:E.294 Water bridges: F:G.179, F:G.181, F:I.220, F:I.220, F:I.220, F:S.241, F:S.241, F:M.242 IMP.19: 23 residues within 4Å: Chain G: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, V.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.294, G.295 Ligands: NAJ.20 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:N.156, G:S.182, G:D.217, G:G.219, G:G.240, G:S.241, G:M.267, G:G.268, G:E.294 Water bridges: G:K.175, G:G.179, G:G.181, G:I.220, G:I.220, G:M.242 IMP.22: 23 residues within 4Å: Chain H: A.52, M.54, N.156, G.181, S.182, I.183, C.184, T.186, D.217, G.218, G.219, M.238, V.239, G.240, S.241, Y.264, G.266, M.267, G.268, S.269, E.294, G.295 Ligands: NAJ.23 19 PLIP interactions: 19 interactions with chain H Hydrogen bonds: H:N.156, H:S.182, H:D.217, H:G.219, H:G.240, H:S.241, H:S.241, H:Y.264, H:M.267, H:G.268, H:E.294 Water bridges: H:G.179, H:G.181, H:I.220, H:I.220, H:I.220, H:S.241, H:S.241, H:M.242

8 x NAJ: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)(Non-covalent)

NAJ.2: 24 residues within 4Å: Chain A: K.77, A.105, D.127, S.128, S.129, H.130, S.133, V.136, N.156, G.177, I.178, G.179, C.184, T.186, M.267, G.268, E.294 Chain G: V.28, L.29, P.30, S.319, G.322, L.323 Ligands: IMP.1 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain G Hydrogen bonds: A:K.77, A:A.105, A:D.127, A:S.129, A:S.129, A:S.129, A:S.133, A:N.156, A:G.177, A:G.179, G:S.319, G:L.323 Water bridges: A:S.53 pi-Stacking: A:H.130 NAJ.5: 21 residues within 4Å: Chain B: D.127, S.128, S.129, H.130, S.133, V.136, N.156, G.177, I.178, G.179, C.184, T.186, M.267, G.268 Chain F: V.28, L.29, P.30, S.319, G.322, L.323 Ligands: IMP.4 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:D.127, B:D.127, B:S.129, B:S.129, B:S.129, B:S.133, B:V.136, B:N.156, B:G.177, B:G.179, F:S.319 Water bridges: B:S.53 pi-Stacking: B:H.130 NAJ.8: 24 residues within 4Å: Chain C: K.77, A.105, D.127, S.128, S.129, H.130, S.133, V.136, N.156, G.177, I.178, G.179, C.184, T.186, M.267, G.268, E.294 Chain E: V.28, L.29, P.30, S.319, G.322, L.323 Ligands: IMP.7 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:K.77, C:A.105, C:D.127, C:S.129, C:S.129, C:S.129, C:S.133, C:N.156, C:G.177, C:G.179, E:S.319, E:L.323 Water bridges: C:S.53 pi-Stacking: C:H.130 NAJ.11: 21 residues within 4Å: Chain D: D.127, S.128, S.129, H.130, S.133, V.136, N.156, G.177, I.178, G.179, C.184, T.186, M.267, G.268 Chain H: V.28, L.29, P.30, S.319, G.322, L.323 Ligands: IMP.10 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain H Hydrogen bonds: D:D.127, D:D.127, D:S.129, D:S.129, D:S.129, D:S.133, D:V.136, D:N.156, D:G.177, D:G.179, H:S.319 Water bridges: D:S.53 pi-Stacking: D:H.130 NAJ.14: 24 residues within 4Å: Chain A: V.28, L.29, P.30, S.319, G.322, L.323 Chain E: K.77, A.105, D.127, S.128, S.129, H.130, S.133, V.136, N.156, G.177, I.178, G.179, C.184, T.186, M.267, G.268, E.294 Ligands: IMP.13 14 PLIP interactions: 2 interactions with chain A, 12 interactions with chain E Hydrogen bonds: A:S.319, A:L.323, E:K.77, E:A.105, E:D.127, E:S.129, E:S.129, E:S.129, E:S.133, E:N.156, E:G.177, E:G.179 Water bridges: E:S.53 pi-Stacking: E:H.130 NAJ.17: 21 residues within 4Å: Chain D: V.28, L.29, P.30, S.319, G.322, L.323 Chain F: D.127, S.128, S.129, H.130, S.133, V.136, N.156, G.177, I.178, G.179, C.184, T.186, M.267, G.268 Ligands: IMP.16 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:D.127, F:D.127, F:S.129, F:S.129, F:S.129, F:S.133, F:V.136, F:N.156, F:G.177, F:G.179, D:S.319 Water bridges: F:S.53 pi-Stacking: F:H.130 NAJ.20: 24 residues within 4Å: Chain C: V.28, L.29, P.30, S.319, G.322, L.323 Chain G: K.77, A.105, D.127, S.128, S.129, H.130, S.133, V.136, N.156, G.177, I.178, G.179, C.184, T.186, M.267, G.268, E.294 Ligands: IMP.19 14 PLIP interactions: 12 interactions with chain G, 2 interactions with chain C Hydrogen bonds: G:K.77, G:A.105, G:D.127, G:S.129, G:S.129, G:S.129, G:S.133, G:N.156, G:G.177, G:G.179, C:S.319, C:L.323 Water bridges: G:S.53 pi-Stacking: G:H.130 NAJ.23: 21 residues within 4Å: Chain B: V.28, L.29, P.30, S.319, G.322, L.323 Chain H: D.127, S.128, S.129, H.130, S.133, V.136, N.156, G.177, I.178, G.179, C.184, T.186, M.267, G.268 Ligands: IMP.22 13 PLIP interactions: 12 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:D.127, H:D.127, H:S.129, H:S.129, H:S.129, H:S.133, H:V.136, H:N.156, H:G.177, H:G.179, B:S.319 Water bridges: H:S.53 pi-Stacking: H:H.130

8 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: G.179, P.180, G.181, C.184 Chain G: E.348, S.349, H.350 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain A Metal complexes: G:E.348, G:S.349, A:G.179, A:G.181, A:C.184 K.6: 7 residues within 4Å: Chain B: G.179, P.180, G.181, C.184 Chain F: E.348, S.349, H.350 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain F Metal complexes: B:G.179, B:G.181, B:C.184, F:E.348, F:S.349 K.9: 7 residues within 4Å: Chain C: G.179, P.180, G.181, C.184 Chain E: E.348, S.349, H.350 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain C Metal complexes: E:E.348, E:S.349, C:G.179, C:G.181, C:C.184 K.12: 7 residues within 4Å: Chain D: G.179, P.180, G.181, C.184 Chain H: E.348, S.349, H.350 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain H Metal complexes: D:G.179, D:G.181, D:C.184, H:E.348, H:S.349 K.15: 7 residues within 4Å: Chain A: E.348, S.349, H.350 Chain E: G.179, P.180, G.181, C.184 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Metal complexes: E:G.179, E:G.181, E:C.184, A:E.348, A:S.349 K.18: 7 residues within 4Å: Chain D: E.348, S.349, H.350 Chain F: G.179, P.180, G.181, C.184 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain D Metal complexes: F:G.179, F:G.181, F:C.184, D:E.348, D:S.349 K.21: 7 residues within 4Å: Chain C: E.348, S.349, H.350 Chain G: G.179, P.180, G.181, C.184 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain G Metal complexes: C:E.348, C:S.349, G:G.179, G:G.181, G:C.184 K.24: 7 residues within 4Å: Chain B: E.348, S.349, H.350 Chain H: G.179, P.180, G.181, C.184 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain B Metal complexes: H:G.179, H:G.181, H:C.184, B:E.348, B:S.349

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with NAD and IMP. To be Published

Release Date

2014-08-06

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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