SMTL ID : 4x3z.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-tetramer

Ligands

4 x XMP: XANTHOSINE-5'-MONOPHOSPHATE(Non-covalent)

XMP.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: NAD.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.156, A:T.186, A:G.219, A:G.240, A:S.241, A:Y.264, A:M.267, A:G.268, A:E.294 Water bridges: A:N.156, A:K.175, A:G.179, A:G.181, A:I.220, A:I.220, A:M.242 XMP.5: 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: NAD.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.156, B:T.186, B:G.219, B:G.240, B:S.241, B:Y.264, B:M.267, B:G.268, B:E.294 Water bridges: B:N.156, B:K.175, B:G.179, B:G.181, B:I.220, B:I.220, B:M.242 XMP.9: 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: NAD.10 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:N.156, C:T.186, C:G.219, C:G.240, C:S.241, C:Y.264, C:M.267, C:G.268, C:E.294 Water bridges: C:N.156, C:K.175, C:G.179, C:G.181, C:I.220, C:I.220, C:M.242 XMP.13: 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: NAD.14 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:N.156, D:T.186, D:G.219, D:G.240, D:S.241, D:Y.264, D:M.267, D:G.268, D:E.294 Water bridges: D:N.156, D:K.175, D:G.179, D:G.181, D:I.220, D:I.220, D:M.242

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 19 residues within 4Å: Chain A: A.106, D.127, S.128, S.129, H.130, S.133, N.156, G.177, I.178, G.179, T.186, M.267, G.268, E.294 Chain C: V.28, L.29, P.30, G.322 Ligands: XMP.1 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.127, A:S.129, A:S.129, A:S.133, A:N.156, A:G.177, A:G.179, C:G.322 Water bridges: A:A.105, A:S.129, A:S.129, A:H.130, A:K.175, A:E.294, C:L.323 Salt bridges: A:H.130, A:H.130 pi-Stacking: A:H.130, A:H.130 NAD.6: 19 residues within 4Å: Chain B: A.106, D.127, S.128, S.129, H.130, S.133, N.156, G.177, I.178, G.179, T.186, M.267, G.268, E.294 Chain D: V.28, L.29, P.30, G.322 Ligands: XMP.5 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:D.127, B:S.129, B:S.129, B:S.133, B:N.156, B:G.177, B:G.179, D:G.322 Water bridges: B:A.105, B:S.129, B:S.129, B:H.130, B:K.175, B:E.294, D:L.323 Salt bridges: B:H.130, B:H.130 pi-Stacking: B:H.130, B:H.130 NAD.10: 19 residues within 4Å: Chain B: V.28, L.29, P.30, G.322 Chain C: A.106, D.127, S.128, S.129, H.130, S.133, N.156, G.177, I.178, G.179, T.186, M.267, G.268, E.294 Ligands: XMP.9 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.127, C:S.129, C:S.129, C:S.133, C:N.156, C:G.177, C:G.179, B:G.322 Water bridges: C:A.105, C:S.129, C:S.129, C:H.130, C:K.175, C:E.294, B:L.323 Salt bridges: C:H.130, C:H.130 pi-Stacking: C:H.130, C:H.130 NAD.14: 19 residues within 4Å: Chain A: V.28, L.29, P.30, G.322 Chain D: A.106, D.127, S.128, S.129, H.130, S.133, N.156, G.177, I.178, G.179, T.186, M.267, G.268, E.294 Ligands: XMP.13 19 PLIP interactions: 2 interactions with chain A, 17 interactions with chain D Hydrogen bonds: A:G.322, D:D.127, D:S.129, D:S.129, D:S.133, D:N.156, D:G.177, D:G.179 Water bridges: A:L.323, D:A.105, D:S.129, D:S.129, D:H.130, D:K.175, D:E.294 Salt bridges: D:H.130, D:H.130 pi-Stacking: D:H.130, D:H.130

4 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: G.179, P.180, G.181, C.184 Chain C: E.348, S.349, H.350 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Metal complexes: C:E.348, C:S.349, A:G.179, A:G.181, A:C.184 K.7: 7 residues within 4Å: Chain B: G.179, P.180, G.181, C.184 Chain D: E.348, S.349, H.350 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Metal complexes: D:E.348, D:S.349, B:G.179, B:G.181, B:C.184 K.11: 7 residues within 4Å: Chain B: E.348, S.349, H.350 Chain C: G.179, P.180, G.181, C.184 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:G.179, C:G.181, C:C.184, B:E.348, B:S.349 K.15: 7 residues within 4Å: Chain A: E.348, S.349, H.350 Chain D: G.179, P.180, G.181, C.184 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Metal complexes: A:E.348, A:S.349, D:G.179, D:G.181, D:C.184

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

PO4.4: 6 residues within 4Å: Chain A: M.6, L.7 Chain C: K.11, T.198, A.201, D.202 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:M.6, A:L.7, C:D.202 Water bridges: A:H.5, A:L.7 Salt bridges: C:K.11 PO4.8: 6 residues within 4Å: Chain B: M.6, L.7 Chain D: K.11, T.198, A.201, D.202 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:M.6, B:L.7, D:D.202 Water bridges: B:H.5, B:L.7 Salt bridges: D:K.11 PO4.12: 6 residues within 4Å: Chain B: K.11, T.198, A.201, D.202 Chain C: M.6, L.7 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:D.202, C:M.6, C:L.7 Salt bridges: B:K.11 Water bridges: C:H.5, C:L.7 PO4.16: 6 residues within 4Å: Chain A: K.11, T.198, A.201, D.202 Chain D: M.6, L.7 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:M.6, D:L.7, A:D.202 Water bridges: D:H.5, D:L.7 Salt bridges: A:K.11

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 XMP and NAD. to be published

Release Date

2014-12-10

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Inosine-5'-monophosphate dehydrogenase

Related Entries With Identical Sequence