SMTL ID : 6d5k.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 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, EPE.11 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:S.14, C:K.24, A:R.136, A:R.136, A:R.140 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: B12.3 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.136, B:R.136, B:R.140 pi-Cation interactions: B:R.136, B:R.136 pi-Stacking: 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, EPE.25 7 PLIP interactions: 2 interactions with chain F, 5 interactions with chain D Hydrogen bonds: F:S.14, F:K.24, D:R.136, D:R.136, D:R.140 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: B12.17 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:R.136, E:R.136, E:R.140 pi-Cation interactions: E:R.136, E:R.136 pi-Stacking: D:F.29

4 x B12: COBALAMIN(Non-covalent)

B12.2: 22 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, M.185 Chain C: S.15, F.17, V.32, D.36, Q.68, G.71, S.72, A.75, Y.88 Ligands: 5AD.1, EPE.11 15 PLIP interactions: 7 interactions with chain C, 8 interactions with chain A, Hydrophobic interactions: C:V.32, C:V.32, C:D.36, C:A.75, C:Y.88, A:L.113, A:F.116, A:F.167, A:F.167 Hydrogen bonds: C:S.72, C:S.72, A:I.117, A:I.117, A:R.136, A:S.163 B12.3: 14 residues within 4Å: Chain A: V.32, D.36, Q.68, S.72 Chain B: L.113, T.114, F.116, I.117, R.132, R.136, S.163, D.164, F.167 Ligands: 5AD.6 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:F.116, B:F.116, B:F.167, B:F.167, A:V.32, A:D.36 Hydrogen bonds: B:I.117, B:I.117, B:R.132, B:R.132, B:R.136, B:D.164, B:D.164, A:S.72, A:S.72 B12.16: 22 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, M.185 Chain F: S.15, F.17, V.32, D.36, Q.68, G.71, S.72, A.75, Y.88 Ligands: 5AD.15, EPE.25 15 PLIP interactions: 7 interactions with chain F, 8 interactions with chain D, Hydrophobic interactions: F:V.32, F:V.32, F:D.36, F:A.75, F:Y.88, D:L.113, D:F.116, D:F.167, D:F.167 Hydrogen bonds: F:S.72, F:S.72, D:I.117, D:I.117, D:R.136, D:S.163 B12.17: 14 residues within 4Å: Chain D: V.32, D.36, Q.68, S.72 Chain E: L.113, T.114, F.116, I.117, R.132, R.136, S.163, D.164, F.167 Ligands: 5AD.20 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain D, Hydrophobic interactions: E:F.116, E:F.116, E:F.167, E:F.167, D:V.32, D:D.36 Hydrogen bonds: E:I.117, E:I.117, E:R.132, E:R.132, E:D.164, D:S.72, D:S.72

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

SO4.4: 4 residues within 4Å: Chain A: H.54, T.55, F.56, Y.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.55, A:F.56 Salt bridges: A:H.54 SO4.5: 1 residues within 4Å: Chain A: K.87 No protein-ligand interaction detected (PLIP) SO4.7: 4 residues within 4Å: Chain B: H.54, T.55, F.56, Y.172 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.55, B:F.56, B:Y.172 Salt bridges: B:H.54 SO4.8: 1 residues within 4Å: Chain B: K.157 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.157 SO4.12: 5 residues within 4Å: Chain C: H.54, T.55, F.56, Y.172, K.176 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.55, C:F.56, C:Y.172 Salt bridges: C:H.54, C:K.176 SO4.13: 5 residues within 4Å: Chain C: K.92, A.93, N.154 Chain F: A.93 Ligands: SO4.27 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C Salt bridges: F:K.157 Hydrogen bonds: C:A.93, C:N.154 SO4.18: 4 residues within 4Å: Chain D: H.54, T.55, F.56, Y.172 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.55, D:F.56, D:Y.172 Salt bridges: D:H.54 SO4.19: 1 residues within 4Å: Chain D: K.87 No protein-ligand interaction detected (PLIP) SO4.21: 4 residues within 4Å: Chain E: H.54, T.55, F.56, Y.172 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.55, E:F.56 Salt bridges: E:H.54 SO4.22: 1 residues within 4Å: Chain E: K.157 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:K.157 SO4.26: 5 residues within 4Å: Chain F: H.54, T.55, F.56, Y.172, K.176 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:T.55, F:F.56, F:Y.172, F:Y.172 Salt bridges: F:H.54, F:K.176 SO4.27: 5 residues within 4Å: Chain C: A.93 Chain F: K.92, A.93, N.154 Ligands: SO4.13 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:A.93, F:N.154 Salt bridges: C:K.157

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

ATP.9: 14 residues within 4Å: Chain B: T.6, K.7, T.8, G.9, S.14, S.15, K.24, F.29 Chain C: R.136, E.139, R.140, N.160 Ligands: MG.10, MG.14 18 PLIP interactions: 7 interactions with chain B, 11 interactions with chain C Hydrogen bonds: B:T.6, B:K.7, B:G.9, B:S.15, C:R.136, C:R.136, C:R.140, C:N.160, C:N.160 Water bridges: B:K.24, C:R.136, C:R.136, C:N.160 Salt bridges: B:K.24, B:K.24, C:R.136 pi-Cation interactions: C:R.136, C:R.136 ATP.23: 14 residues within 4Å: Chain E: T.6, K.7, T.8, G.9, S.14, S.15, K.24, F.29 Chain F: R.136, E.139, R.140, N.160 Ligands: MG.24, MG.28 19 PLIP interactions: 8 interactions with chain E, 11 interactions with chain F Hydrogen bonds: E:T.6, E:K.7, E:T.8, E:G.9, E:S.15, F:R.136, F:R.136, F:R.140, F:N.160, F:N.160 Water bridges: E:K.24, F:R.136, F:R.136, F:N.160 Salt bridges: E:K.24, E:K.24, F:R.136 pi-Cation interactions: F:R.136, F:R.136

4 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 3 residues within 4Å: Chain B: I.4 Chain C: D.164 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.24: 3 residues within 4Å: Chain E: I.4 Chain F: D.164 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 EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 9 residues within 4Å: Chain A: R.136, N.160, D.164 Chain C: K.11, S.14, S.15, K.24 Ligands: 5AD.1, B12.2 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:N.160, A:D.164, C:S.15, C:S.15 Salt bridges: A:R.136, C:K.24 EPE.25: 9 residues within 4Å: Chain D: R.136, N.160, D.164 Chain F: K.11, S.14, S.15, K.24 Ligands: 5AD.15, B12.16 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:N.160, D:D.164, F:S.15, F:S.15 Salt bridges: D:R.136, F:K.24

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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