SMTL ID : 2w6v.1

Structure of Human deoxy Hemoglobin A in complex with Xenon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-mer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 17 residues within 4Å: Chain A: Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:F.46, A:K.61, A:K.61, A:V.62, A:A.65, A:L.83, A:L.83, A:L.86, A:L.91, A:V.93, A:V.93, A:F.98, A:F.98, A:L.101, A:L.101, A:L.136 Salt bridges: A:H.45, A:K.61, A:K.61 pi-Stacking: A:H.58 Metal complexes: A:H.87 HEM.7: 19 residues within 4Å: Chain B: L.31, F.41, F.42, H.63, K.66, V.67, A.70, F.71, F.85, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: XE.10 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:L.31, B:F.41, B:F.41, B:F.42, B:F.42, B:F.42, B:K.66, B:V.67, B:F.71, B:F.85, B:L.88, B:L.88, B:L.91, B:L.96, B:V.98, B:V.98, B:F.103, B:L.106, B:L.141 Water bridges: B:K.66, B:K.66 Salt bridges: B:K.66 pi-Stacking: B:H.63 Metal complexes: B:H.92 HEM.12: 20 residues within 4Å: Chain C: M.32, T.39, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.105, L.136 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:Y.42, C:K.61, C:K.61, C:V.62, C:L.83, C:L.86, C:L.91, C:L.91, C:N.97, C:F.98, C:F.98, C:L.101, C:L.101, C:L.105, C:L.136 Water bridges: C:K.61 Salt bridges: C:H.45, C:K.61 pi-Stacking: C:H.58 Metal complexes: C:H.87 HEM.19: 18 residues within 4Å: Chain D: L.31, F.41, F.42, F.45, H.63, K.66, V.67, A.70, F.71, F.85, L.88, H.92, L.96, V.98, N.102, F.103, L.106, L.141 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:F.41, D:F.41, D:F.42, D:K.66, D:V.67, D:A.70, D:F.85, D:L.88, D:L.88, D:L.96, D:L.96, D:V.98, D:F.103, D:L.106, D:L.106, D:L.141 Salt bridges: D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: A.26, E.27, E.30, S.49, H.50, G.51, S.52, V.55 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.30, A:S.49, A:G.51, A:S.52 Water bridges: A:E.27, A:E.27 GOL.13: 9 residues within 4Å: Chain C: A.26, E.27, E.30, S.49, H.50, G.51, S.52, V.55, K.56 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.49, C:G.51, C:S.52 Water bridges: C:E.27 GOL.20: 5 residues within 4Å: Chain C: F.36, K.99, L.100 Chain D: R.104, N.108 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.104, D:N.108, D:N.108, C:K.99 Water bridges: C:H.103

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

SO4.3: 2 residues within 4Å: Chain A: Y.24, H.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.24, A:Y.24 Salt bridges: A:H.112 SO4.8: 5 residues within 4Å: Chain A: F.36, L.100, H.103 Chain B: R.104, N.108 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.104, B:N.108 Water bridges: B:Q.131, B:Q.131 Salt bridges: A:H.103 SO4.9: 3 residues within 4Å: Chain B: E.26, H.116, H.117 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.117 Water bridges: B:E.26, B:H.116, B:H.116, B:H.117, B:H.117 Salt bridges: B:H.116, B:H.117 SO4.14: 6 residues within 4Å: Chain C: K.16, H.112, L.113, P.114, A.115, E.116 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.115, C:E.116 SO4.21: 1 residues within 4Å: Chain D: T.87 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.87 Water bridges: D:T.87

10 x XE: XENON(Non-covalent)

XE.4: 2 residues within 4Å: Chain A: W.14, F.128 No protein-ligand interaction detected (PLIP) XE.5: 3 residues within 4Å: Chain A: W.14, Y.24, L.105 No protein-ligand interaction detected (PLIP) XE.6: 5 residues within 4Å: Chain A: F.43, F.46, Q.54, V.55, H.58 No protein-ligand interaction detected (PLIP) XE.10: 3 residues within 4Å: Chain B: F.103, G.107 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) XE.11: 1 residues within 4Å: Chain B: A.10 No protein-ligand interaction detected (PLIP) XE.16: 2 residues within 4Å: Chain C: W.14, F.128 No protein-ligand interaction detected (PLIP) XE.17: 3 residues within 4Å: Chain C: Y.24, L.105, L.109 No protein-ligand interaction detected (PLIP) XE.18: 6 residues within 4Å: Chain C: L.29, F.33, F.43, F.46, V.55, H.58 No protein-ligand interaction detected (PLIP) XE.24: 3 residues within 4Å: Chain D: F.103, V.134, V.137 No protein-ligand interaction detected (PLIP) XE.25: 5 residues within 4Å: Chain D: G.24, L.28, G.64, V.67, L.106 No protein-ligand interaction detected (PLIP)

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

PO4.15: 2 residues within 4Å: Chain C: S.49, H.50 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.49, C:H.50 PO4.22: 2 residues within 4Å: Chain D: H.116, H.117 5 PLIP interactions: 5 interactions with chain D Water bridges: D:E.26, D:R.30, D:H.116 Salt bridges: D:H.116, D:H.117 PO4.23: 5 residues within 4Å: Chain D: L.78, D.79, N.80, L.81, K.82 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.81, D:K.82 Water bridges: D:G.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Savino, C. et al., Pattern of Cavities in Globins: The Case of Human Hemoglobin. Biopolymers (2009)

Release Date

2009-04-28

Peptides

HEMOGLOBIN SUBUNIT ALPHA: AC
HEMOGLOBIN SUBUNIT BETA: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

HEMOGLOBIN SUBUNIT ALPHA

HEMOGLOBIN SUBUNIT BETA

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