SMTL ID : 2qjo.1

crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.45, R.55, P.57 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.45, A:R.45 Salt bridges: A:R.45, A:R.55 SO4.2: 1 residues within 4Å: Chain A: N.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.106 Water bridges: A:D.129 SO4.3: 4 residues within 4Å: Chain A: H.44, R.45, R.81 Chain B: A.321 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.81 Salt bridges: A:H.44, A:R.45, A:R.81 SO4.7: 4 residues within 4Å: Chain A: D.318 Chain B: H.44, R.45, R.81 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.44, B:R.45, B:R.81 SO4.14: 3 residues within 4Å: Chain D: R.45, R.55, P.57 4 PLIP interactions: 4 interactions with chain D Water bridges: D:R.45, D:R.45 Salt bridges: D:R.45, D:R.55 SO4.15: 1 residues within 4Å: Chain D: N.106 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.106 SO4.16: 4 residues within 4Å: Chain D: H.44, R.45, R.81 Chain E: A.321 4 PLIP interactions: 4 interactions with chain D Water bridges: D:R.81 Salt bridges: D:H.44, D:R.45, D:R.81 SO4.20: 4 residues within 4Å: Chain D: D.318 Chain E: H.44, R.45, R.81 3 PLIP interactions: 3 interactions with chain E Salt bridges: E:H.44, E:R.45, E:R.81

6 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.4: 18 residues within 4Å: Chain A: Y.190, F.203, T.205, D.207, R.221, A.223, G.234, G.235, F.236, E.250, E.254, R.279, R.282, T.285, Y.327, E.328, H.330 Chain C: Y.199 23 PLIP interactions: 20 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Y.190, A:T.205, A:D.207, A:F.236, A:E.250, A:E.254, A:R.279, A:R.279, A:R.282, A:T.287, A:E.328, C:Y.199 Water bridges: A:R.221, A:G.234, A:G.234, A:R.249 Salt bridges: A:R.221, A:R.279, A:R.282 pi-Stacking: A:F.236, A:F.236, C:Y.199, C:Y.199 APR.8: 18 residues within 4Å: Chain B: Y.190, F.203, T.205, D.207, R.221, A.223, G.234, G.235, F.236, E.250, E.254, R.279, R.282, T.285, Y.327, E.328, H.330 Chain E: Y.199 24 PLIP interactions: 20 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:Y.190, B:Y.190, B:D.207, B:F.236, B:E.250, B:E.254, B:R.279, B:R.279, B:T.287, B:E.328, E:Y.199, E:Y.199 Water bridges: B:R.221, B:R.221, B:R.249, B:E.254 Salt bridges: B:R.221, B:R.279, B:R.282, B:R.282 pi-Stacking: B:F.236, B:F.236, E:Y.199, E:Y.199 APR.11: 19 residues within 4Å: Chain A: Y.199 Chain C: Y.190, F.203, T.205, D.207, R.221, A.223, G.234, G.235, F.236, E.250, E.254, R.279, S.280, R.282, T.285, T.287, E.328, H.330 21 PLIP interactions: 17 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:Y.190, C:Y.190, C:D.207, C:F.236, C:E.250, C:E.254, C:R.279, C:S.280, C:S.280, A:Y.199, A:Y.199 Water bridges: C:R.221, C:R.221 Salt bridges: C:R.221, C:R.279, C:R.282, C:R.282 pi-Stacking: C:F.236, C:F.236, A:Y.199, A:Y.199 APR.17: 18 residues within 4Å: Chain D: Y.190, F.203, T.205, D.207, R.221, A.223, G.234, G.235, F.236, E.250, E.254, R.279, R.282, T.285, Y.327, E.328, H.330 Chain F: Y.199 24 PLIP interactions: 20 interactions with chain D, 4 interactions with chain F Hydrogen bonds: D:Y.190, D:Y.190, D:D.207, D:F.236, D:E.250, D:E.254, D:E.254, D:R.279, D:R.279, D:R.282, D:E.328, F:Y.199, F:Y.199 Water bridges: D:R.221, D:G.234, D:G.234, D:R.249 Salt bridges: D:R.221, D:R.279, D:R.282 pi-Stacking: D:F.236, D:F.236, F:Y.199, F:Y.199 APR.21: 18 residues within 4Å: Chain B: Y.199 Chain E: Y.190, F.203, T.205, D.207, R.221, A.223, G.234, G.235, F.236, E.250, E.254, R.279, R.282, T.285, Y.327, E.328, H.330 21 PLIP interactions: 18 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:Y.190, E:D.207, E:F.236, E:E.250, E:E.254, E:R.279, E:R.279, E:Y.327, E:E.328, B:Y.199 Water bridges: E:R.221, E:R.221, E:R.249 Salt bridges: E:R.221, E:R.279, E:R.282, E:R.282 pi-Stacking: E:F.236, E:F.236, B:Y.199, B:Y.199 APR.24: 19 residues within 4Å: Chain D: Y.199 Chain F: Y.190, F.203, T.205, D.207, R.221, A.223, G.234, G.235, F.236, E.250, E.254, R.279, S.280, R.282, T.285, T.287, E.328, H.330 20 PLIP interactions: 17 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:Y.190, F:D.207, F:F.236, F:E.250, F:E.254, F:R.279, F:S.280, F:S.280, F:T.287, D:Y.199 Water bridges: F:R.221, F:R.221 Salt bridges: F:R.221, F:R.279, F:R.282, F:R.282 pi-Stacking: F:F.236, F:F.236, D:Y.199, D:Y.199

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

NAD.5: 24 residues within 4Å: Chain A: Y.12, I.13, G.14, R.15, F.16, H.20, H.23, G.42, S.43, D.82, W.83, S.86, D.87, W.90, G.112, H.113, K.115, Y.120, Y.121, G.134, H.135, Y.136, F.139 Ligands: POP.6 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.121 Hydrogen bonds: A:R.15, A:F.16, A:W.83, A:D.87, A:D.87, A:H.113, A:H.135, A:Y.136, A:Y.136, A:F.139 Water bridges: A:S.43, A:S.43, A:S.118, A:Y.121, A:Y.121, A:S.141 Salt bridges: A:R.15, A:R.15, A:H.23 pi-Stacking: A:W.90, A:W.90 NAD.9: 26 residues within 4Å: Chain B: Y.12, I.13, G.14, R.15, F.16, H.20, H.23, G.42, S.43, D.82, W.83, L.84, S.86, D.87, W.90, G.112, H.113, K.115, Y.120, Y.121, L.122, G.134, H.135, Y.136, F.139 Ligands: POP.10 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.121 Hydrogen bonds: B:R.15, B:F.16, B:G.42, B:W.83, B:D.87, B:H.113, B:K.115, B:Y.121, B:Y.121, B:Y.136, B:Y.136 Water bridges: B:R.15, B:H.23, B:S.43, B:S.43, B:D.82, B:T.133, B:S.141 Salt bridges: B:R.15, B:R.15, B:H.23, B:K.115 pi-Stacking: B:W.90, B:W.90 NAD.12: 24 residues within 4Å: Chain C: Y.12, I.13, G.14, R.15, F.16, H.20, H.23, G.42, S.43, D.82, W.83, L.84, S.86, D.87, W.90, G.112, H.113, K.115, Y.120, Y.121, H.135, Y.136, F.139 Ligands: POP.13 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Y.121 Hydrogen bonds: C:R.15, C:F.16, C:D.82, C:W.83, C:W.83, C:H.113, C:H.113, C:Y.121, C:H.135, C:Y.136, C:Y.136, C:F.139 Water bridges: C:S.43, C:S.43 Salt bridges: C:R.15, C:R.15 pi-Stacking: C:W.90, C:W.90 NAD.18: 24 residues within 4Å: Chain D: Y.12, I.13, G.14, R.15, F.16, H.20, H.23, G.42, S.43, D.82, W.83, S.86, D.87, W.90, G.112, H.113, K.115, Y.120, Y.121, G.134, H.135, Y.136, F.139 Ligands: POP.19 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:Y.121 Hydrogen bonds: D:Y.12, D:R.15, D:F.16, D:W.83, D:D.87, D:H.113, D:Y.121, D:Y.136, D:Y.136, D:F.139 Water bridges: D:S.43, D:S.43, D:S.118, D:Y.121, D:T.133, D:S.141 Salt bridges: D:R.15, D:R.15, D:H.23 pi-Stacking: D:W.90, D:W.90 NAD.22: 26 residues within 4Å: Chain E: Y.12, I.13, G.14, R.15, F.16, H.20, H.23, G.42, S.43, D.82, W.83, L.84, S.86, D.87, W.90, G.112, H.113, K.115, Y.120, Y.121, L.122, G.134, H.135, Y.136, F.139 Ligands: POP.23 27 PLIP interactions: 27 interactions with chain E Hydrophobic interactions: E:Y.121 Hydrogen bonds: E:Y.12, E:R.15, E:F.16, E:G.42, E:W.83, E:D.87, E:D.87, E:H.113, E:K.115, E:Y.121, E:Y.121, E:Y.136, E:Y.136 Water bridges: E:R.15, E:H.23, E:T.26, E:S.43, E:S.43, E:S.43, E:S.141 Salt bridges: E:R.15, E:R.15, E:H.23, E:K.115 pi-Stacking: E:W.90, E:W.90 NAD.25: 24 residues within 4Å: Chain F: Y.12, I.13, G.14, R.15, F.16, H.20, H.23, G.42, S.43, D.82, W.83, L.84, S.86, D.87, W.90, G.112, H.113, K.115, Y.120, Y.121, H.135, Y.136, F.139 Ligands: POP.26 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:Y.121 Hydrogen bonds: F:Y.12, F:R.15, F:F.16, F:W.83, F:W.83, F:D.87, F:H.113, F:H.113, F:H.113, F:Y.136, F:Y.136, F:F.139 Water bridges: F:S.43, F:S.43 Salt bridges: F:R.15, F:R.15 pi-Stacking: F:W.90, F:W.90

6 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.6: 7 residues within 4Å: Chain A: R.15, K.115, S.140, S.141, T.142, R.145 Ligands: NAD.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.140, A:S.141, A:T.142, A:T.142 Water bridges: A:S.141 Salt bridges: A:R.15, A:K.115, A:R.145 POP.10: 8 residues within 4Å: Chain B: R.15, R.51, K.115, S.140, S.141, T.142, R.145 Ligands: NAD.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.141, B:S.141, B:T.142, B:T.142, B:T.142 Salt bridges: B:R.15, B:R.51, B:K.115, B:K.115, B:R.145 POP.13: 7 residues within 4Å: Chain C: R.15, K.115, S.140, S.141, T.142, R.145 Ligands: NAD.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.141, C:S.141, C:T.142, C:T.142 Salt bridges: C:R.15, C:K.115, C:R.145 POP.19: 7 residues within 4Å: Chain D: R.15, K.115, S.140, S.141, T.142, R.145 Ligands: NAD.18 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.140, D:S.141, D:T.142 Water bridges: D:S.141 Salt bridges: D:R.15, D:K.115, D:R.145 POP.23: 8 residues within 4Å: Chain E: R.15, R.51, K.115, S.140, S.141, T.142, R.145 Ligands: NAD.22 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:S.141, E:S.141, E:T.142, E:T.142 Salt bridges: E:R.15, E:R.51, E:K.115, E:K.115, E:R.145 POP.26: 7 residues within 4Å: Chain F: R.15, K.115, S.140, S.141, T.142, R.145 Ligands: NAD.25 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:S.141, F:S.141, F:T.142, F:T.142, F:T.142 Salt bridges: F:R.15, F:K.115, F:R.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, N. et al., Bifunctional NMN Adenylyltransferase/ADP-Ribose Pyrophosphatase: Structure and Function in Bacterial NAD Metabolism. Structure (2008)

Release Date

2008-03-11

Peptides

Bifunctional NMN adenylyltransferase/Nudix hydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Bifunctional NMN adenylyltransferase/Nudix hydrolase