SMTL ID : 7m1t.1

Crystal structure of an archaeal CNNM, MtCorB, with C-terminal deletion in complex with Mg2+-ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.26 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: S.21, G.22, S.25, S.71, N.75, G.110, E.111 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.21, A:S.21, A:S.71, A:G.110, A:E.111 MG.10: 3 residues within 4Å: Chain A: H.293 Chain B: E.311 Ligands: ATP.18 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: E.311 Chain B: H.293 Ligands: ATP.8 No protein-ligand interaction detected (PLIP)

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

SO4.2: 7 residues within 4Å: Chain A: R.47, K.48, G.49, A.50, K.51, A.52, R.131 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.49, A:A.50, A:K.51, A:A.52 Salt bridges: A:K.48, A:R.131 SO4.12: 6 residues within 4Å: Chain B: K.48, G.49, A.50, K.51, A.52, R.131 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.49, B:K.51, B:A.52 Salt bridges: B:R.131

10 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.3: 8 residues within 4Å: Chain A: F.20, F.24, G.70, I.73, A.74, F.135, F.136, L.139 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.20, A:I.73, A:F.136, A:F.136 UMQ.4: 6 residues within 4Å: Chain A: F.23, L.125, R.128, V.129, P.132 Ligands: UMQ.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.23, A:V.129 UMQ.5: 9 residues within 4Å: Chain A: I.69, I.73, K.138, L.139, L.140, Y.141, P.142, V.143 Ligands: UMQ.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.69, A:P.142, A:V.143 UMQ.6: 11 residues within 4Å: Chain A: Y.141, P.142, V.143, W.145, V.146, T.147, I.150 Chain B: V.108, I.112, M.116 Ligands: UMQ.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.142, A:V.146, A:V.146 UMQ.7: 8 residues within 4Å: Chain A: L.19, F.20, F.23, R.131, P.132, F.135, F.136 Ligands: UMQ.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.19, A:F.23 Hydrogen bonds: A:R.131 Salt bridges: A:R.131 UMQ.13: 10 residues within 4Å: Chain B: F.23, S.26, G.113, P.114, Y.117, L.125, R.128, V.129, P.132 Ligands: UMQ.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.117, B:Y.117, B:V.129 UMQ.14: 8 residues within 4Å: Chain B: L.19, F.20, F.23, R.131, P.132, F.135, F.136 Ligands: UMQ.13 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.19, B:F.23, B:P.132, B:F.136 Hydrogen bonds: B:R.131 UMQ.15: 9 residues within 4Å: Chain A: V.104, L.107, V.108 Chain B: Y.141, P.142, V.143, W.145, V.146 Ligands: UMQ.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.143, B:V.146 Hydrogen bonds: B:W.145 UMQ.16: 7 residues within 4Å: Chain B: F.20, F.24, G.70, I.73, A.74, F.136, L.139 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.20, B:F.20, B:F.20, B:A.74, B:F.136, B:L.139 UMQ.17: 6 residues within 4Å: Chain A: L.107 Chain B: I.69, I.73, L.140, V.143 Ligands: UMQ.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.73, B:V.143

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

ATP.8: 20 residues within 4Å: Chain A: T.207, D.211, V.212, V.213, F.233, S.234, R.235, I.236, P.237, M.294, I.307, V.308, T.309, E.311, D.312 Chain B: R.235, K.253, H.293 Ligands: MG.11, ATP.18 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain A Salt bridges: B:R.235, B:K.253, B:K.253, B:H.293, A:R.235 Hydrogen bonds: A:T.207, A:T.207, A:V.213, A:S.234, A:R.235, A:R.235, A:T.309, A:D.312 pi-Stacking: A:F.233, A:F.233 ATP.18: 19 residues within 4Å: Chain A: R.235, K.253, H.293 Chain B: T.207, D.211, V.212, V.213, F.233, S.234, R.235, I.236, P.237, M.294, I.307, T.309, E.311, D.312 Ligands: ATP.8, MG.10 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:V.213, B:V.213, B:S.234, B:T.309 Salt bridges: B:R.235, A:K.253, A:K.253, A:H.293 pi-Stacking: B:F.233, B:F.233

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 12 residues within 4Å: Chain A: R.58, S.59, T.60, D.61, R.157, P.158, G.159, V.160 Chain B: E.169, E.172, W.173, V.176 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.60, A:D.61, A:R.157, B:E.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y.S. et al., Crystal structure of an archaeal CorB magnesium transporter. Nat Commun (2021)

Release Date

2021-06-16

Peptides

Hemolysin, contains CBS domains: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Hemolysin, contains CBS domains