SMTL ID : 6d5x.2 (1 other biounit)

Structure of Human ATP:Cobalamin Adenosyltransferase bound to ATP, Adenosylcobalamin, and Triphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

4 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.1: 9 residues within 4Å: Chain A: R.136, E.139, R.140 Chain C: S.14, S.15, K.24, F.29 Ligands: B12.2, 3PO.5 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:S.14, C:K.24, A:R.136, A:R.136, A:R.140 Water bridges: C:S.14, C:S.15, A:R.136, A:R.136 pi-Cation interactions: A:R.136, A:R.136 5AD.6: 5 residues within 4Å: Chain A: F.29 Chain B: R.136, E.139, R.140 Ligands: B12.7 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.136, B:R.136, B:E.139, B:R.140 pi-Cation interactions: B:R.136, B:R.136 pi-Stacking: A:F.29, A:F.29 5AD.15: 9 residues within 4Å: Chain D: R.136, E.139, R.140 Chain F: S.14, S.15, K.24, F.29 Ligands: B12.16, 3PO.19 12 PLIP interactions: 4 interactions with chain F, 8 interactions with chain D Hydrogen bonds: F:S.14, F:K.24, D:R.136, D:R.136, D:E.139, D:R.140 Water bridges: F:S.14, F:S.15, D:R.136, D:R.136 pi-Cation interactions: D:R.136, D:R.136 5AD.20: 5 residues within 4Å: Chain D: F.29 Chain E: R.136, E.139, R.140 Ligands: B12.21 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain E pi-Stacking: D:F.29, D:F.29 Hydrogen bonds: E:R.136, E:R.136, E:R.140 pi-Cation interactions: E:R.136, E:R.136

4 x B12: COBALAMIN(Non-covalent)

B12.2: 21 residues within 4Å: Chain A: L.113, T.114, A.115, F.116, I.117, R.132, R.136, S.163, D.164, F.167 Chain C: S.15, F.17, V.32, D.36, Q.68, G.71, S.72, A.75, Y.88 Ligands: 5AD.1, 3PO.5 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain C, Hydrophobic interactions: A:F.116, A:F.116, A:F.167, A:F.167, C:F.17, C:V.32, C:D.36, C:A.75, C:Y.88 Hydrogen bonds: A:I.117, A:I.117, A:R.132, A:R.136, A:D.164, C:S.72 Water bridges: A:D.164, C:Q.68, C:G.71 B12.7: 16 residues within 4Å: Chain A: V.32, D.36, Q.68, S.72, A.75 Chain B: L.113, T.114, A.115, F.116, I.117, R.132, R.136, S.163, D.164, F.167 Ligands: 5AD.6 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B, Hydrophobic interactions: A:V.32, A:D.36, A:A.75, B:F.167, B:F.167 Hydrogen bonds: A:Q.68, B:I.117, B:I.117, B:R.132, B:R.136, B:D.164 B12.16: 21 residues within 4Å: Chain D: L.113, T.114, A.115, F.116, I.117, R.132, R.136, S.163, D.164, F.167 Chain F: S.15, F.17, V.32, D.36, Q.68, G.71, S.72, A.75, Y.88 Ligands: 5AD.15, 3PO.19 20 PLIP interactions: 12 interactions with chain D, 8 interactions with chain F, Hydrophobic interactions: D:F.116, D:F.116, D:F.167, D:F.167, F:F.17, F:V.32, F:D.36, F:A.75, F:Y.88 Hydrogen bonds: D:I.117, D:I.117, D:R.132, D:R.136, D:D.164, D:D.164, F:S.72 Water bridges: D:T.114, D:D.164, F:Q.68, F:G.71 B12.21: 16 residues within 4Å: Chain D: V.32, D.36, Q.68, S.72, A.75 Chain E: L.113, T.114, A.115, F.116, I.117, R.132, R.136, S.163, D.164, F.167 Ligands: 5AD.20 10 PLIP interactions: 6 interactions with chain E, 4 interactions with chain D, Hydrophobic interactions: E:F.167, E:F.167, D:V.32, D:D.36, D:A.75 Hydrogen bonds: E:I.117, E:I.117, E:R.132, E:D.164, D:Q.68

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

SO4.3: 5 residues within 4Å: Chain A: H.54, T.55, F.56, Y.106, Y.172 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.55, A:T.55, A:F.56 Salt bridges: A:H.54, A:K.176 SO4.8: 5 residues within 4Å: Chain B: H.54, T.55, F.56, Y.106, Y.172 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.55, B:T.55, B:F.56, B:Y.172 Salt bridges: B:H.54 SO4.11: 5 residues within 4Å: Chain C: G.53, H.54, T.55, F.56, Y.172 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.54, C:T.55, C:T.55, C:F.56 SO4.12: 5 residues within 4Å: Chain C: A.93, N.154 Chain F: A.93, K.157 Ligands: SO4.26 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain C Water bridges: F:K.157, F:K.157 Salt bridges: F:K.157 Hydrogen bonds: C:A.93, C:N.154 SO4.13: 1 residues within 4Å: Chain C: K.87 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.87 SO4.17: 5 residues within 4Å: Chain D: H.54, T.55, F.56, Y.106, Y.172 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.55, D:F.56, D:Y.106, D:Y.172 Salt bridges: D:H.54, D:K.176 SO4.22: 5 residues within 4Å: Chain E: H.54, T.55, F.56, Y.106, Y.172 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:T.55, E:T.55, E:T.55, E:F.56, E:Y.106 Salt bridges: E:H.54 SO4.25: 5 residues within 4Å: Chain F: G.53, H.54, T.55, F.56, Y.172 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:H.54, F:T.55, F:T.55, F:T.55, F:F.56, F:Y.172 SO4.26: 5 residues within 4Å: Chain C: A.93, K.157 Chain F: A.93, N.154 Ligands: SO4.12 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:A.93, F:N.154 Water bridges: C:K.157, C:K.157 Salt bridges: C:K.157 SO4.27: 1 residues within 4Å: Chain F: K.87 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:K.87

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 3 residues within 4Å: Chain A: R.136, N.160 Ligands: 3PO.5 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain B: K.24 Chain C: N.160 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain D: R.136, N.160 Ligands: 3PO.19 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Ligands: ATP.23 No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain E: K.24 Chain F: N.160 Ligands: ATP.23 No protein-ligand interaction detected (PLIP)

2 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.5: 12 residues within 4Å: Chain A: R.136, N.160, D.164 Chain C: K.7, T.8, G.9, F.13, S.14, K.24 Ligands: 5AD.1, B12.2, MG.4 12 PLIP interactions: 5 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:K.7, C:S.14, A:N.160, A:N.160 Water bridges: C:S.15, A:R.136, A:R.136, A:R.136, A:R.136 Salt bridges: C:K.24, C:K.24, A:R.136 3PO.19: 12 residues within 4Å: Chain D: R.136, N.160, D.164 Chain F: K.7, T.8, G.9, F.13, S.14, K.24 Ligands: 5AD.15, B12.16, MG.18 11 PLIP interactions: 5 interactions with chain F, 6 interactions with chain D Hydrogen bonds: F:T.8, F:S.14, D:N.160 Water bridges: F:S.15, D:R.136, D:R.136, D:R.136, D:R.136 Salt bridges: F:K.24, F:K.24, D:R.136

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

ATP.9: 16 residues within 4Å: Chain B: Y.5, T.6, K.7, T.8, G.9, F.13, S.14, S.15, K.24, F.29 Chain C: R.136, E.139, R.140, N.160 Ligands: MG.10, MG.14 22 PLIP interactions: 8 interactions with chain B, 14 interactions with chain C Hydrogen bonds: B:T.6, B:T.6, B:K.7, B:G.9, B:S.14, B:S.15, C:R.136, C:R.136, C:E.139, C:R.140, C:N.160, C:D.164 Salt bridges: B:K.24, B:K.24, C:R.136 Water bridges: C:R.132, C:R.136, C:R.136, C:R.136, C:R.136 pi-Cation interactions: C:R.136, C:R.136 ATP.23: 16 residues within 4Å: Chain E: Y.5, T.6, K.7, T.8, G.9, F.13, S.14, S.15, K.24, F.29 Chain F: R.136, E.139, R.140, N.160 Ligands: MG.24, MG.28 21 PLIP interactions: 13 interactions with chain F, 8 interactions with chain E Hydrogen bonds: F:R.136, F:R.136, F:R.140, F:N.160, F:D.164, E:T.6, E:K.7, E:T.8, E:G.9, E:S.14, E:S.15 Water bridges: F:R.132, F:R.136, F:R.136, F:R.136, F:R.136 Salt bridges: F:R.136, E:K.24, E:K.24 pi-Cation interactions: F:R.136, F:R.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campanello, G.C. et al., Sacrificial Cobalt-Carbon Bond Homolysis in Coenzyme B12as a Cofactor Conservation Strategy. J. Am. Chem. Soc. (2018)

Release Date

2018-10-10

Peptides

Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial

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